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Suite ID Suite version Date of first commit of the suite Tool IDs Description EDAM topic(s) EDAM operation(s) Suite runs on main servers bio.tools (if available) Conda id biii Status Availability across Galaxies
0.0.1+galaxy0 sgwb_astro_tool SGWB 21
ipython
To update
UseGalaxy.eu1
0.0.1+galaxy0 plot_tools_astro_tool Plot Tools 0
pandas
To update
0.0.2+galaxy0 hess_astro_tool Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope 6
ipython
To update
UseGalaxy.eu1
0.0.1+galaxy0 desi_legacy_survey_astro_tool Tool to query Legacy Survey data 0
astropy
To update
0.0.1+galaxy0 cta_astro_tool Basic simulation of CTA telescope observations using gammapy package 3
unzip
To update
UseGalaxy.eu1
0.0.2+galaxy0 crbeam_astro_tool CRbeam 0
crbeam
To update
0.2.0+galaxy0 astropy_fits2bitmap astropy_fits2csv astropy_fitsinfo AstropyTools library contains Galaxy tools for elementary Astrophysical operations 39
astropy
To update
UseGalaxy.cz3 UseGalaxy.eu3
0.10.1 astronomical_archives Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy 165
astropy
To update
UseGalaxy.cz1 UseGalaxy.eu1
0.1.0+galaxy0 xlsx2tsv Convert an xlsx file to a tabular 0
pandas
To update
UseGalaxy.eu1
2.2.4 virsorter VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. Metagenomics Taxonomic classification 1032
virsorter
Up-to-date
UseGalaxy.eu1
1.2.1 vibrant Virus Identification By iteRative ANnoTation Metagenomics Microbial ecology Sequence assembly Molecular interactions, pathways and networks Endocrinology and metabolism Sequence trimming Scaffolding Genome annotation 57
vibrant
Up-to-date
UseGalaxy.eu1
3.0.1 dr_curve A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses 0
r-drc
To update
0.1.0+galaxy0 tt_baseline Toxicity prediction using QSAR models 0
pandas
To update
0.2 singularity_scriptrunner suite_scripting 0
To update
2.4.1 saqc System for automated Quality Control 0
saqc
To update
UseGalaxy.eu1
2.1.11 phabox_cherry phabox_contamination phabox_end_to_end phabox_phagcn phabox_phamer phabox_phatyp phabox_phavip phabox_tree phabox_votu Identify and analyze phage contigs in metagenomic data Metagenomics Microbial ecology Sequence assembly Taxonomy Sequence assembly Taxonomic classification Visualisation 0
phabox
Up-to-date
5.18.0 omero_dataset_to_plate omero_filter omero_get_id omero_get_value omero_import omero_metadata_import omero_roi_import Interact with an OMERO.server using omero-py and ezomero. Imaging Data visualisation Image analysis 0
To update
UseGalaxy.eu3
0.4.0 msh2vtu shp2msh A suite of tools for OpenGeoSys (ogs) 0
ogstools
To update
6.5.3 ogs_addlayer ogs_extractboundary ogs_extractsurface ogs_generatestructuredmesh ogs_identifysubdomains ogs_simulation A suite of tools for OpenGeoSys (ogs) 0
To update
0.3.0 longORF obtain longest ORF in six-frame translations 0
To update
0.1.0+galaxy0 lm_get_projects Lambda-Miner Tools 0
pandas
To update
1.3.3 iphop_predict Integrated Phage Host Prediction Sample comparison 0
iphop
Up-to-date
1.8.0 genomad_end_to_end Identify virus and plasmid genomes from nucleotide sequences Sequence analysis Sequence annotation Taxonomic classification 4974
genomad
To update
UseGalaxy.eu1 UseGalaxy.fr1
2.1 dfpl_predict dfpl_train Galaxy wrapper for deepFPlearn. 0
deepfplearn
Up-to-date
1.3.6 dfast Prokaryotic genome annotation Nucleic acid structure analysis Genomics Sequence analysis Genome annotation 0
dfast
Up-to-date
1.0.3 checkv_end_to_end Assess quality of single-contig viral genomes Metagenomics Sequence assembly Metagenomic sequencing Mapping Sequence assembly Validation Read mapping 114
checkv
Up-to-date
UseGalaxy.eu1
4.2.0 FROGS_affiliation_filters FROGS_affiliation_postprocess FROGS_affiliation_stats FROGS_biom_to_stdBiom FROGS_biom_to_tsv FROGS_cluster_filters FROGS_cluster_stats FROGS_clustering FROGS_demultiplex FROGSSTAT_DESeq2_Preprocess FROGSSTAT_DESeq2_Visualisation FROGSFUNC_step2_functions FROGSFUNC_step3_pathways FROGSFUNC_step1_placeseqs FROGS_itsx FROGS_normalisation FROGSSTAT_Phyloseq_Alpha_Diversity FROGSSTAT_Phyloseq_Beta_Diversity FROGSSTAT_Phyloseq_Sample_Clustering FROGSSTAT_Phyloseq_Composition_Visualisation FROGSSTAT_Phyloseq_Import_Data FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance FROGSSTAT_Phyloseq_Structure_Visualisation FROGS_preprocess FROGS_remove_chimera FROGS_taxonomic_affiliation FROGS_Tree FROGS_tsv_to_biom Suite for metabarcoding analysis 181987
frogs
To update
UseGalaxy.fr18
2.16.0 blastxml_to_tabular get_species_taxids ncbi_blastdbcmd_info ncbi_blastdbcmd_wrapper ncbi_blastn_wrapper ncbi_blastp_wrapper ncbi_blastx_wrapper ncbi_convert2blastmask_wrapper ncbi_deltablast_wrapper ncbi_dustmasker_wrapper ncbi_makeblastdb ncbi_makeprofiledb ncbi_psiblast_wrapper ncbi_rpsblast_wrapper ncbi_rpstblastn_wrapper ncbi_segmasker_wrapper ncbi_tblastn_wrapper ncbi_tblastx_wrapper NCBI BLAST+ 4410694
blast
Up-to-date
UseGalaxy.be16 UseGalaxy.cz16 UseGalaxy.eu16 UseGalaxy.fr15 UseGalaxy.no15 UseGalaxy.or16
0.0.3 make_nr Make a FASTA file non-redundant Molecular biology Sequence analysis Sequence alignment Genome annotation 0
biopython
To update
0.1.2 blastxml_to_top_descr Make table of top BLAST match descriptions Sequence analysis Sequence alignment Sequence annotation 793332
python
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
0.3.0 blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files Nucleic acid sites, features and motifs Gene functional annotation Nucleic acid sequence analysis 65029
biopython
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
0.0.11 blast2go Maps BLAST results to GO annotation terms Nucleic acid sites, features and motifs Gene functional annotation 3208
b2g4pipe
To update
UseGalaxy.cz1 UseGalaxy.no1
0.0.5 uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server 0
omero-py
To update
0.0.2 revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. 1734
samtools
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
20240214 omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements 0
fiji
To update
20230809 omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels 0
fiji
To update
20240521 omero_get_full_images Get full images from omero 0
fiji
To update
0.2.0 omero_get_children_ids Get omero id of children of an omero object id 0
omero-py
To update
20230623 omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down 0
fiji
To update
20221216 measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index 0
fiji
To update
20241213.2 max_projections_stack_and_upload_omero Combine images from max projections to stack and upload to the omero server 0
Fiji
To update
20231221 incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server 0
Fiji
To update
20241220 hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack 0
Fiji
To update
0.0.2 getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension 0
pysam
To update
0.11.1+galaxy1 fromgtfTobed12 Convert GTF files to BED12 format 0
gffutils
To update
0.0.2 fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. 0
pysam
To update
0.9.3 cooler_balance cooler_cload_tabix cooler_csort_tabix cooler_makebins cooler_zoomify cooler different tools to process Hi-C from mirnylab 1602
htslib
To update
UseGalaxy.cz4 UseGalaxy.eu5 UseGalaxy.or4
SNVPhyl suite defining all dependencies for SNVPhyl 0
To update
1.8.2 verify_map Checks the mapping quality of all BAM(s) 0
snvphyl-tools
Up-to-date
1.8.2 vcf2snvalignment Generates multiple alignment of variant calls 0
snvphyl-tools
Up-to-date
1.8.2 snvmatrix Generate matrix of SNV distances 0
snvphyl-tools
Up-to-date
1.8.2 positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. 0
snvphyl-tools
Up-to-date
1.8.2 positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. 0
snvphyl-tools
Up-to-date
1.8.2 findrepeat Find repetitive regions on a reference genome using MUMMer 0
snvphyl-tools
Up-to-date
1.8.2 filtervcf SNVPhyl filter_vcf 0
snvphyl-tools
Up-to-date
1.8.2 filterstat SNVPhyl filter_stats 0
snvphyl-tools
Up-to-date
1.8.2 filterdensity Filter out position based on distance between SNVs 0
snvphyl-tools
Up-to-date
1.8.2 consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment 0
snvphyl-tools
Up-to-date
6.6.1 xtb_molecular_optimization Performs semiempirical molecular optimization. 786
xtb
To update
UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
0.2.0 waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. Metabolomics Standardisation and normalisation 894
r-recetox-waveica
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
table_pandas_arithmetics table_pandas_rename_column table_pandas_rename_columns_regex table_pandas_transform table_scipy_interpolate Tools to manipulate and analyze data tables. 0
scipy
To update
UseGalaxy.eu5
0.8.0 spec2vec_similarity spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. Proteomics experiment Metabolomics Natural language processing Proteomics Spectrum calculation Spectral library search Database search Natural product identification 345
spec2vec
Up-to-date
UseGalaxy.eu2 UseGalaxy.or2
3.0.0 rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. 204
python
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
0.4.1 riassigner riassigner_from_comment Metabolomics Compound libraries and screening Data submission, annotation and curation Standardisation and normalisation 906
riassigner
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu2 UseGalaxy.fr1 UseGalaxy.or2
0.5.4 retip_apply retip_descriptors retip_filter_rt retip_train Metabolomics Proteomics experiment Machine learning Cheminformatics Chemistry Retention time prediction Spectrum calculation Deisotoping Formatting Deposition 0
To update
1.0.0 rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results 120
pandas
To update
UseGalaxy.eu1 UseGalaxy.or1
1.0.0 rem_complex Removes molecular coordination complexes. 297
pandas
To update
UseGalaxy.eu1 UseGalaxy.or1
0.10.0 recetox_xmsannotator_advanced Expression profile pathway mapping Structure comparison Isotopic distributions calculation Annotation 399
r-recetox-xmsannotator
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
v3.5.2 recetox_msfinder Metabolomics Annotation 438
To update
UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
3.5.1 rcx_boxplot recetox-boxplot is a tool for plotting boxplots from a tabular/csv/parquet data file. 0
r-ggplot2
To update
0.13.4 recetox_aplcms_align_features recetox_aplcms_compute_clusters recetox_aplcms_compute_template recetox_aplcms_correct_time recetox_aplcms_generate_feature_table recetox_aplcms_merge_known_table recetox_aplcms_recover_weaker_signals recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. Metabolomics Chromatographic alignment Quantification Peak detection Feature extraction Alignment 7914
r-recetox-aplcms
Up-to-date
UseGalaxy.cz8 UseGalaxy.eu8 UseGalaxy.fr8 UseGalaxy.or8
0.1.0+galaxy0 rcx-tk Tools to process metadata or alkane files. 0
rcx-tk
To update
UseGalaxy.eu1
1.3.0 ramclustr ramclustr_define_experiment Metabolomics Imputation Standardisation and normalisation Clustering Correlation 2577
r-ramclustr
To update
UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
0.2 query Execute an SQL statement on a set of tables 0
click
To update
5.2.1 qcxms_getres qcxms_neutral_run qcxms_production_run QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). 109080
To update
UseGalaxy.eu3 UseGalaxy.or3
0.1.0+galaxy2 mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. 0
lxml
To update
0.1.0 msp_merge 0
matchms
To update
0.4.0 msmetaenhancer Metabolomics Compound libraries and screening Data submission, annotation and curation Annotation Standardisation and normalisation 861
msmetaenhancer
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
2.0.0 ms2deepscore_config_generator ms2deepscore_similarity ms2deepscore_training Mass spectra similarity scoring using a trained ms2deepscore model. Proteomics experiment Machine learning Metabolomics Small molecules Compound libraries and screening Spectrum calculation Spectral library search Network analysis 0
ms2deepscore
To update
UseGalaxy.eu3
1.0.0 target_screen use_theoretical_mz_annotations 558
pandas
To update
UseGalaxy.eu2 UseGalaxy.or1
1.1.2 mfassignr_findRecalSeries mfassignr_histnoise mfassignr_isofiltr mfassignr_kmdnoise mfassignr_mfassign mfassignr_mfassignCHO mfassignr_recal mfassignr_recallist mfassignr_snplot The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements Proteomics experiment Molecular interactions, pathways and networks Workflows Visualisation 150
r-mfassignr
Up-to-date
UseGalaxy.eu9 UseGalaxy.or9
0.27.0 matchms_add_key matchms_convert matchms_matchms_export_skyline_transition_list matchms_filtering matchms_fingerprint_similarity matchms_formatter matchms_metadata_export matchms_metadata_match matchms_metadata_merge matchms_networking matchms_remove_key matchms_remove_spectra matchms_spectral_similarity matchms_split matchms_subsetting Searching, filtering and converting mass spectral libraries. Metabolomics Spectral library search Format validation Filtering 14358
matchms
To update
UseGalaxy.cz9 UseGalaxy.eu14 UseGalaxy.fr11 UseGalaxy.or14
2.6+galaxy0 isolib Create an isotopic pattern library for given compounds and adducts. 189
bioconductor-metabocoreutils
To update
UseGalaxy.eu1 UseGalaxy.or1
1.0.1 gc_derivatization In silico derivatization for GC. 66
gc-meox-tms
Up-to-date
UseGalaxy.eu1 UseGalaxy.or1
3.1.1 filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. 0
openbabel
To update
3.0.20230403 biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. Small molecules Endocrinology and metabolism Metabolomics Carbohydrates NMR Metabolic pathway prediction PTM site prediction Natural product identification 201
biotransformer
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
1.16.0 bioconductor_scp scp is a package for the single cell proteomics data processing. Proteomics experiment Proteomics Visualisation Expression analysis 0
scp
bioconductor-scp
Up-to-date
UseGalaxy.eu1 UseGalaxy.or1
2.32.0 bioconductor_msnbase_centroid bioconductor_msnbase_smooth_chromatogram bioconductor_msnbase_smooth_mz MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. Proteomics Proteomics experiment Data management Data visualisation Data handling Visualisation 0
bioconductor-msnbase
Up-to-date
UseGalaxy.eu3
1.0.0+galaxy1 ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets 2812
ucsc-cell-browser
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
4.0.0 seurat_convert seurat_dim_plot seurat_export_cellbrowser seurat_filter_cells seurat_find_clusters seurat_find_markers seurat_find_neighbours seurat_find_variable_genes seurat_hover_locator seurat_integration seurat_map_query seurat_normalise_data seurat_plot seurat_read10x seurat_run_pca seurat_run_tsne seurat_run_umap seurat_scale_data seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 17069
seurat-scripts
To update
UseGalaxy.eu14 UseGalaxy.fr19 UseGalaxy.or14
1.0.2 scpred_get_feature_space scpred_get_std_output scpred_predict_labels scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 75
scpred-cli
To update
UseGalaxy.eu4
1.6.4 scmap_get_std_output scmap_index_cell scmap_index_cluster scmap_preprocess_sce scmap_scmap_cell scmap_scmap_cluster scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. 342
scmap-cli
To update
UseGalaxy.cz1 UseGalaxy.eu7
0.0.5 sceasy_convert Convert scRNA data object between popular formats 5990
r-sceasy
To update
UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
0.0.9 run_sccaf sccaf_asses sccaf_asses_merger sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. 319
sccaf
To update
UseGalaxy.eu4 UseGalaxy.or3
1.10.0 scater_calculate_cpm scater_calculate_qc_metrics scater_filter scater_is_outlier scater_normalize scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. 2163
scater-scripts
To update
UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu6 UseGalaxy.no2 UseGalaxy.or2
1.9.3 anndata_ops scanpy_filter_cells scanpy_filter_genes scanpy_find_cluster scanpy_find_markers scanpy_find_variable_genes scanpy_integrate_bbknn scanpy_integrate_combat scanpy_integrate_harmony scanpy_integrate_mnn scanpy_plot_scrublet scanpy_multiplet_scrublet scanpy_compute_graph scanpy_normalise_data scanpy_parameter_iterator scanpy_plot_embed scanpy_plot_trajectory scanpy_read_10x scanpy_regress_variable scanpy_run_diffmap scanpy_run_dpt scanpy_run_fdg scanpy_run_paga scanpy_run_pca scanpy_run_tsne scanpy_run_umap scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. 190611
scanpy-scripts
To update
UseGalaxy.cz14 UseGalaxy.eu27 UseGalaxy.no13 UseGalaxy.or27
1.8.0 sc3_calc_biology sc3_calc_consens sc3_calc_dists sc3_calc_transfs sc3_estimate_k sc3_kmeans sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. 35
sc3-scripts
To update
UseGalaxy.eu7
0.12.1 pyscenic_aucell pyscenic_binarize pyscenic_ctx pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ 0
To update
0.1.4 monocle3_create monocle3_diffExp monocle3_learnGraph monocle3_orderCells monocle3_partition monocle3_plotCells monocle3_preprocess monocle3_reduceDim monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. 16443
monocle3-cli
To update
UseGalaxy.eu9 UseGalaxy.or9
0.2.8 garnett_check_markers garnett_classify_cells garnett_get_feature_genes garnett_get_std_output garnett_train_classifier garnett_transform_markers update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 81
garnett-cli
To update
UseGalaxy.eu7
1.0.4 dropletutils_empty_drops dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 8419
dropletutils-scripts
To update
UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
1.4.0+galaxy3 score_genes_aucell decoupler_pathway_inference decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities 366
decoupler
To update
UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
v0.0.2+galaxy2 retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home 5146
wget
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
v0.0.4+galaxy0 hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects 1609
hca-matrix-downloader
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
1.6.3+galaxy1 celltypist_predict celltypist - Automated cell type annotation 0
celltypist
To update
1.1.1 ct_build_cell_ontology_dict ct_check_labels ct_combine_tool_outputs ct_downsample_cells ct_get_consensus_outputs ct_get_empirical_dist ct_get_tool_perf_table ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis 27
cell-types-analysis
To update
UseGalaxy.eu6
0.0.1+galaxy6 _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data 3411
scipy
To update
UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
0.25.1+galaxy0 fastq_filter_n fastq_trim_poly_at Set of tools for handling fastq files 0
fastq_utils
To update
0.0.14+galaxy0 cshl_fastq_quality_trimmer FASTQ trimmer based on quality 0
fastx_toolkit
To update
1.0+galaxy0 fastq_pair Paired-end fastq pairer 0
fastq-pair
To update
1.52.0+galaxy0 _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. 11168
atlas-gene-annotation-manipulation
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
0.4.4 fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. 0
atlas-fastq-provider
To update
1.6.1+galaxy2 _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC 5248
scxa-plots
To update
UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
0.1.0 smithsonian_volcanoes Retrieve data from Volcanoes of the World (VOTW) Database 0
python
To update
0.1.0 shyft_longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees 188
python
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
1.3.1 psy_maps Visualization of regular geographical data on a map with psyplot 1291
python
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
0.2.0 mean_per_zone Creates a png image showing statistic over areas as defined in the vector file 49
python
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
2.0 ctsm_fates EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model 1278
fates-emerald
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
0.2.0 cds_essential_variability Get Copernicus Essential Climate Variables for assessing climate variability 718
python
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
1.0.2 eodie Earth Observation Data Information Extractor 135
eodie
To update
UseGalaxy.cz1 UseGalaxy.eu1
1.0.2 climate_stripes Create climate stripes from a tabular input file 1404
python
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
2.1.3 cesm Community Earth System Model (CESM) 42
cesm
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu1
cdo
2.0.0 cdo_info cdo_operations CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. 684
To update
UseGalaxy.cz2 UseGalaxy.eu2
0.1.0 cads Copernicus Atmosphere Data Store (ADS) 156
python
To update
UseGalaxy.cz1 UseGalaxy.eu1
c3s
0.3.0 c3s Copernicus Climate Change Service (C3S) 1377
python
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
0.1.0 zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. 78
r-base
To update
UseGalaxy.eu1
1.6.1 xmlstarlet Tool to convert a xml file from one metadata standard to another 309
xmlstarlet
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
0.1.1 vigiechiro_bilanenrichipf vigiechiro_bilanenrichirp vigiechiro_idcorrect_2ndlayer vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. 45702
To update
UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.fr4 UseGalaxy.no4
0.1.0 terrabyte_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from terrabyte (https://docs.terrabyte.lrz.de/). 30
r-base
To update
UseGalaxy.eu1
0.0.2 stoceps_filteringsp stoceps_glm stoceps_glm_group stoceps_maketablecarrer stoceps_trend_indic Tools to analyse STOC data. 1014
To update
UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.no5
0.0.1 srs_diversity_maps srs_global_indices srs_process_data srs_spectral_indices srs_pca srs_preprocess_s2 srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 945
r-base
To update
UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.fr7 UseGalaxy.or4
1.2.2 spocc_occ Get species occurences data 2417
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
0.2.15 sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. 9
r-base
To update
UseGalaxy.eu1
1.3.0 retrieve_bold Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers 30
r-base
To update
UseGalaxy.eu1
1.5 regionalgam_ab_index regionalgam_autocor_acf regionalgam_flight_curve regionalgam_glmmpql regionalgam_gls_adjusted regionalgam_gls regionalgam_plot_trend 1294
r-mgcv
To update
UseGalaxy.be6 UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.fr7 UseGalaxy.no7
1.0 otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. 171
r-base
To update
UseGalaxy.eu1
1.0 otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. 297
r-base
To update
UseGalaxy.eu1
0.9.3 bgc_canyon_b Robust Estimation of Open Ocean CO2 Variables and Nutrient Concentrations From T, S, and O2 Data Using Bayesian Neural Networks 0
r-base
To update
UseGalaxy.eu1
0.2 tool_odv The tool merges various datasets with a common vocabulary and creates a single generic ODV spreadsheet in an automatic way. 0
To update
UseGalaxy.eu1
0.1.15 argo_getdata copernicusmarine divand_full_analysis Access, process, and visualise oceanographic data for the Earth System 297
copernicusmarine
To update
UseGalaxy.eu3
0.0.2 obisindicators obis_data Compute biodiveristy indicators for marine data from obis 1122
r-base
To update
UseGalaxy.cz1 UseGalaxy.eu2 UseGalaxy.fr1 UseGalaxy.or1
0.1.0 iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa 102
pandas
To update
UseGalaxy.eu1
0.9.3.5 sanntis_marine The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data 327
sanntis
To update
UseGalaxy.eu1 UseGalaxy.or1
0.1.0+galaxy0 data_paper_from_EML This tool derived from the R Shiny App MetaShRIMPS <https://github.com/TanguyGen/metaCure> is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. 72
r-base
To update
UseGalaxy.eu1
1.0 interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file 210
r-getopt
To update
UseGalaxy.eu1
0.2.0 hirondelle_crim This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. 708
r-base
To update
UseGalaxy.eu1
3.0.0 gdal_gdal_merge gdal_gdal_translate gdal_gdaladdo gdal_gdalbuildvrt gdal_gdalinfo gdal_gdalwarp gdal_ogr2ogr gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. 3961
To update
UseGalaxy.cz8 UseGalaxy.eu8 UseGalaxy.fr8 UseGalaxy.no8
0.1.0 landcover_subindicator Access, process, visualise oceanographic data for the Earth System 6
numpy
To update
UseGalaxy.eu1
2022.3.0 timeseries_extraction xarray_coords_info xarray_mapplot xarray_metadata_info xarray_netcdf2netcdf xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. 19443
xarray
To update
UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.fr5 UseGalaxy.no2 UseGalaxy.or2
0.0.0 tool_anonymization ecology_homogeneity_normality ecology_beta_diversity ecology_link_between_var ecology_presence_abs_abund ecology_stat_presence_abs Explore data through multiple statistical tools 3756
r-tangles
To update
UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.fr6
1.0.0 aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences 17580
r-bioseq
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
0.0.0 cb_dissim cb_ivr cb_div Compute indicators for turnover boulders fields 648
r-base
To update
UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3
2.0 harmonize_insitu_to_netcdf Process in-situ and biogechemical oceanographic Argo or Glider data for the Earth System 57
To update
UseGalaxy.eu1
0.5.0 aquainfra_ogc_api_processes Wrapper for OGC API Processes developed in the AquaINFRA project. 771
r-base
To update
UseGalaxy.eu1
1.0 aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. 831
To update
UseGalaxy.eu1
1.20.0 ab1_fastq_converter Tool to convert ab1 files into FASTQ files 187071
bioconductor-sangerseqr
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
0.0.2 pampa_communitymetrics pampa_presabs pampa_glmcomm pampa_glmsp pampa_plotglm Tools to compute and analyse biodiversity metrics 6642
To update
UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.no4 UseGalaxy.or5
0.1.0+galaxy0 Map_shp Mean_geom bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). 267
r-base
To update
UseGalaxy.eu3 UseGalaxy.fr3
0.1.0+galaxy0 ecoregion_brt_analysis ecoregion_GeoNearestNeighbor ecoregion_cluster_estimate ecoregion_clara_cluster ecoregion_eco_map ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. 1926
r-base
To update
UseGalaxy.cz5 UseGalaxy.eu6 UseGalaxy.fr5
0.1.0+galaxy0 annotations_template eal_table_template eal_templates eml2eal eml_validate entities_template geo_cov_template makeeml raster_template taxo_cov_template vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa 1854
r-base
To update
UseGalaxy.cz2 UseGalaxy.eu11 UseGalaxy.fr9
2.5.1 yac Clips 3' adapters for small RNA sequencing reads. 0
python
To update
UseGalaxy.fr1
2.1+galaxy0 xpore_dataprep xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing 0
xpore
To update
1.2.9 wisecondorx_npz_converter wisecondorx_predict wisecondorx_reference_builder WisecondorX 0
wisecondorx
Up-to-date
0.1 varscan_vaf Compute variant allele frequency in vcf files generated by varscan. 0
python
To update
0.6.1 tarfast5 produces a tar.gz archive of fast5 sequence files 0
pigz
To update
UseGalaxy.no1
2.8 sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. 0
bowtie
To update
UseGalaxy.fr1
2.3.1 bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads Microbiology Biology 294
bowtie
To update
UseGalaxy.fr1
3.0.0+galaxy1 sequenzaindex snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza 0
sequenza-utils
To update
UseGalaxy.fr2
3.4.2 overlapping_reads signature Computes the tendency of small RNAs to overlap with each other. 0
pysam
To update
UseGalaxy.fr2
3.1.1 small_rna_maps Generates small read maps from alignment BAM files 0
numpy
To update
UseGalaxy.fr1
1.3.0 small_rna_clusters clusters small rna reads in alignment BAM files 0
pysam
To update
UseGalaxy.fr1
2.2.0 sequence_format_converter various fasta to tabular conversions 0
python
To update
UseGalaxy.fr1
0.1.1 sashimi_plot Generates a sashimi plot from bam files. 0
python
To update
UseGalaxy.fr1
0.7.1+galaxy1 sambamba_sample_or_filter filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM 2508
sambamba
To update
UseGalaxy.fr1 UseGalaxy.or1
extract_transcript_to_gene_map_from_trinity purgegtffrommultichromgenes rsembowtie2 rsembowtie transcript quantification from RNA-Seq data 1424
rsem
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr4 UseGalaxy.no1
2.31.1 edger-repenrich2 repenrich2 Repeat element profiling using bowtie2 aligner 0
To update
2.31.1 edger-repenrich repenrich Repeat element profiling 5523
To update
UseGalaxy.fr2 UseGalaxy.or2
0.22.0 probecoverage computes and plots read coverage of genomic regions by sequencing datasets 0
pysam
To update
UseGalaxy.fr1
0.2.5b9 pindel Pindel detects genome-wide structural variation. 0
pindel
Up-to-date
UseGalaxy.fr1
1.40.0 pathifier pathifier 771
bioconductor-pathifier
To update
UseGalaxy.cz1 UseGalaxy.eu1
1.4.0 oasesoptimiserv Short read assembler 0
oases
To update
UseGalaxy.fr1
3.12.0 mutational_patterns Mutational patterns and signatures in base substitution catalogs 0
bioconductor-mutationalpatterns
To update
1.6 mircounts Generates miRNA count lists from read alignments to mirBase. 4938
tar
To update
UseGalaxy.fr1 UseGalaxy.or1
0.22.0 mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file 0
r-optparse
To update
1.6 manta Structural variant and indel caller for mapped sequencing data 1704
manta
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
1.3 lumpy Find structural variations 0
lumpy-sv
To update
UseGalaxy.fr1
0.2.8+galaxy1 lumpy_smoove vcf2hrdetect Galaxy wrapper of the lumpy-using smoove workflow 0
svtyper
To update
UseGalaxy.fr2
2.8+galaxy0 justgzip Compress fastq sequence files 60
pigz
To update
UseGalaxy.fr1
3.10+galaxy0 justdiff Unix diff 0
diffutils
To update
UseGalaxy.fr1
3.1.3+galaxy0 high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps 0
r-gplots
To update
UseGalaxy.fr1
6.5.7+galaxy0 guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies 21
To update
UseGalaxy.fr1
2.3.9+galaxy1 signature_score Compute signature scores from single cell RNAseq data RNA-Seq analysis Clustering Visualisation Expression analysis 0
r-optparse
To update
1.28.1+galaxy1 scran_normalize Normalize raw counts using scran RNA-Seq analysis Clustering Visualisation Expression analysis 1524
bioconductor-scran
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
4.1.3+galaxy1 mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data RNA-Seq analysis Clustering Visualisation Expression analysis 0
r-optparse
To update
4.3+galaxy1 high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation RNA-Seq analysis Clustering Visualisation Expression analysis 0
r-optparse
To update
4.3.1+galaxy1 single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations RNA-Seq analysis Clustering Visualisation Expression analysis 0
r-optparse
To update
4.3.1+galaxy1 filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data RNA-Seq analysis Clustering Visualisation Expression analysis 0
r-optparse
To update
4.3.1+galaxy1 filter_cells Filter single cell RNAseq data on library depth and number of detected genes RNA-Seq analysis Clustering Visualisation Expression analysis 0
r-optparse
To update
4.3.1+galaxy1 center_scale Center or scale (standardize) data RNA-Seq analysis Clustering Visualisation Expression analysis 0
r-optparse
To update
0.3.2 get_fasta_reference Obtain reference genome sequence. 0
To update
UseGalaxy.fr1
4.1.7.0 filtermutectcalls mergemutectstats mutect2 Find somatic variations 0
gatk4
To update
2.32.0+galaxy0 fishertest Fisher's exact test on two-column hit lists. 0
bioconductor-qvalue
To update
3.1.0 retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers 7
urllib3
To update
UseGalaxy.fr1
3.4.4 ez_histograms ggplot2 histograms and density plots Ecology Data analysis Statistical calculation Visualisation 0
r-ggplot2
To update
UseGalaxy.fr1
0.2 embl2fa Converts EMBL flat format to fasta format 0
To update
1.40.2+galaxy1 deseq2_normalization Normalizes gene hitlists 0
bioconductor-deseq2
To update
UseGalaxy.fr1
0.6.0 cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts 0
r-optparse
To update
UseGalaxy.fr1
1.4.3 cat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. 44196
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
4.1 cherry_pick_fasta Pick fasta sequence with specific header content 0
python
To update
UseGalaxy.fr1
2.0.1 cap3 cap3 wrapper 57300
cap3
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
1.1.1 blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs 0
python
To update
UseGalaxy.fr1
2.7.1 BlastParser_and_hits Parse blast outputs and compile hits 24
python
To update
UseGalaxy.fr1
1.0.1 blast_unmatched Extract unmatched query sequences from blast 0
python
To update
UseGalaxy.fr1
1.1.0 blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs 24
python
To update
UseGalaxy.fr1
3+galaxy0 bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format 0
ucsc-bigwiginfo
To update
UseGalaxy.fr1
377+galaxy1 bigwig_to_bedgraph Converts a bigWig file to bedGraph format 21347
ucsc-bigwigtobedgraph
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
4.1.1 bamparse Generates hit count lists from bam alignments. 0
pysam
To update
UseGalaxy.fr1
1.10+galaxy0 artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis 0
samtools
To update
UseGalaxy.fr1
vmd
vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations 0
To update
1.8.1 pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. 3699
pdbfixer
To update
UseGalaxy.cz1 UseGalaxy.eu1
1.9.7 traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories 297
mdtraj
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
1.9.9 md_slicer A tool for slicing trajectory files using MDTraj. 1958
mdtraj
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
1.9.7 md_converter A tool for interconverting between different MD structure and trajectory file formats. 87539
mdtraj
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
1.0.0 mdanalysis_angle mdanalysis_dihedral mdanalysis_distance mdanalysis_endtoend mdanalysis_extract_rmsd mdanalysis_hbonds mdanalysis_cosine_analysis mdanalysis_ramachandran_protein mdanalysis_ramachandran_plot mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations 12175
mdanalysis
To update
UseGalaxy.be1 UseGalaxy.cz10 UseGalaxy.eu10 UseGalaxy.fr10 UseGalaxy.no10 UseGalaxy.or5
2022 gmx_check gmx_editconf gmx_energy gmx_get_builtin_file gmx_rg gmx_makendx gmx_merge_topology_files gmx_em gmx_restraints gmx_rmsd gmx_rmsf gmx_setup gmx_sim gmx_solvate gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. 634825
gromacs
To update
UseGalaxy.be6 UseGalaxy.cz15 UseGalaxy.eu15 UseGalaxy.fr13 UseGalaxy.no9 UseGalaxy.or8
Free energy tools of BRIDGE. 0
To update
0 gromacs_modify_topology gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. 264
python
To update
UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
18.169.1 packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations 2108
packmol
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
21.10 ambertools_acpype acpype_Amber2Gromacs ambertools_antechamber mmpbsa_mmgbsa ambertools_parmchk2 parmconv tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. 139002
ambertools
To update
UseGalaxy.be1 UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.fr2 UseGalaxy.no5 UseGalaxy.or2
1.5.2 biomd_neqgamma fastpca biomd_extract_clusters biomd_rmsd_clustering Tools for MD analysis 3321
scipy
To update
UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.no3 UseGalaxy.or4
4.2.1 biobb_pytorch_apply_mdae biobb_pytorch_train_mdae biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular [PyTorch](https://pytorch.org/) Python library. 0
biobb_pytorch
To update
2.4_1 bio3d_dccm bio3d_pca bio3d_rmsd bio3d_rmsf bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. 48301
r-bio3d
To update
UseGalaxy.be4 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.no5 UseGalaxy.or4
2.0.4 ZeissLMDconverter Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems 24
shapely
To update
UseGalaxy.eu1
0.1.5 validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. 762
validate-fasta-database
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
2.5.0 uniprotxml_downloader Download UniProt proteome in XML or fasta format 7561
requests
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
6.2.4+galaxy0 unipept Unipept retrieves metaproteomics information Proteomics Proteogenomics Biodiversity Workflows Prediction and recognition Visualisation 20521
python
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
0.2.0 translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column 169
biopython
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
0.1.0 gp_spectrast2tsv Filter from spectraST files to swath input files 0
msproteomicstools
To update
0.1.0 gp_spectrast2spectrast_irt Filter from spectraST files to swath input files 0
msproteomicstools
To update
0.2.4 sixgill_build sixgill_filter sixgill_makefasta sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS 948
sixgill
Up-to-date
UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.fr4 UseGalaxy.no4
0.1.0 scaffold scaffold_export 0
scaffold
To update
1.0.3 regex1 regexColumn1 Use python regular expressions to find and replace text 346416
python
To update
UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
rawtools Raw Tools 1888
rawtools
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
0.3.2 qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type 543
geojson
To update
UseGalaxy.cz1 UseGalaxy.eu1
2.0 quantwiz_iq Isobaric Quantitation using QuantWiz-IQ 90
quantwiz-iq
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
1.1.2 quantp Correlation between protein and transcript abundance 572
r-data.table
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
4.4.1 mztab2tsv Tools using the pyteomics library Proteomics Proteomics experiment Protein identification 276
pyteomics
To update
UseGalaxy.cz1 UseGalaxy.eu1
2.1.4 pyprophet_export pyprophet_merge pyprophet_peptide pyprophet_protein pyprophet_score pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. 10305
pyprophet
To update
UseGalaxy.be5 UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.no6 UseGalaxy.or5
1.1.2 maxquant_ptxqc Quality control reports for MaxQuant results Proteomics Validation 0
r-ptxqc
To update
1.0.3 psmvalidator Validate PSM from Ion Fragmentation 60
To update
UseGalaxy.cz1 UseGalaxy.eu1
0.1.0 psm_eval 0
binaries_for_psm_eval
To update
0.1.0 protxml_to_xls 0
trans_proteomic_pipeline
To update
2021.06.08 proteore_venn_diagram ProteoRE JVenn Diagram 45
python
To update
0.0.8 proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. 2082
proteomiqon-psmstatistics
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu1
0.0.8 proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. 1812
proteomiqon-psmbasedquantification
To update
UseGalaxy.cz1 UseGalaxy.eu1
0.0.7 proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. 267
proteomiqon-proteininference
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu1
0.0.7 proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. 2058
proteomiqon-peptidespectrummatching
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu1
0.0.7 proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. 288
proteomiqon-peptidedb
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu1
0.0.8 proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. 2166
proteomiqon-mzmltomzlite
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu1
0.0.1 proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. 24
proteomiqon-labelfreeproteinquantification
To update
UseGalaxy.cz1 UseGalaxy.eu1
0.0.1 proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. 48
proteomiqon-labeledproteinquantification
To update
UseGalaxy.cz1 UseGalaxy.eu1
0.0.1 proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. 1116
proteomiqon-joinquantpepionswithproteins
To update
UseGalaxy.cz1 UseGalaxy.eu1
0.1.0 translate_bed Translate BED transcript CDS or cDNA in 3 frames 6029
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
0.1.0 retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format 0
To update
0.1 convert_windows_newlines proteinpilot proteinpilot_group_extractor proteinpilot_tabular proteinpilot_xml 0
To update
1.3.2.1 PSMtoSAM PSM to SAM 0
r-base
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UseGalaxy.fr1
CustomProDB Annotation 0
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1.22.0 custom_pro_db CustomProDB 7879
bioconductor-rgalaxy
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UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
1.4.0 pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS 0
r-base
To update
1.3 calc_delta_pi pi_db_split pi_dbspec_align HiRIEF tools 0
python
To update
3.5 batched_set_list_creator percolator percolator_input_converters pout2mzid Percolator 4667
percolator
To update
UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.no4 UseGalaxy.or4
Convert PepXML to Tabular 0
To update
fasta_cli ident_params peptide_shaker search_gui PeptideShaker and SearchGUI 56655
searchgui
To update
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1.0.0 peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files 1974
python
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
2.0.2 pepquery2 pepquery2_index pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation 5247
pepquery
Up-to-date
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1.6.2 pepquery A peptide-centric MS search engine for novel peptide identification and validation. 22305
pepquery
To update
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0.1.3+galaxy1 pep_pointer PepPointer categorizes peptides by their genomic coordinates. 2227
python
To update
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reactome_pathwaymatcher Reactome Pathway Matcher 588
pathwaymatcher
To update
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3.1 AccurateMassSearch AssayGeneratorMetabo BaselineFilter CVInspector ClusterMassTraces ClusterMassTracesByPrecursor CometAdapter ConsensusID ConsensusMapNormalizer DTAExtractor DatabaseFilter DatabaseSuitability DeMeanderize DecoyDatabase Digestor DigestorMotif EICExtractor ERPairFinder Epifany ExternalCalibration FalseDiscoveryRate FeatureFinderCentroided FeatureFinderIdentification FeatureFinderIsotopeWavelet FeatureFinderMRM FeatureFinderMetabo FeatureFinderMetaboIdent FeatureFinderMultiplex FeatureLinkerLabeled FeatureLinkerUnlabeled FeatureLinkerUnlabeledKD FeatureLinkerUnlabeledQT FileConverter FileFilter FileInfo FileMerger FuzzyDiff GNPSExport HighResPrecursorMassCorrector IDConflictResolver IDExtractor IDFileConverter IDFilter IDMapper IDMassAccuracy IDMerger IDPosteriorErrorProbability IDRTCalibration IDRipper IDScoreSwitcher IDSplitter InternalCalibration IsobaricAnalyzer JSONExporter LuciphorAdapter MRMMapper MRMPairFinder MRMTransitionGroupPicker MSFraggerAdapter MSGFPlusAdapter MSstatsConverter MapAlignerIdentification MapAlignerPoseClustering MapAlignerSpectrum MapAlignerTreeGuided MapNormalizer MapRTTransformer MapStatistics MascotAdapter MascotAdapterOnline MassCalculator MassTraceExtractor MetaProSIP MetaboliteSpectralMatcher MultiplexResolver MzMLSplitter MzTabExporter NoiseFilterGaussian NoiseFilterSGolay NovorAdapter NucleicAcidSearchEngine OpenMSDatabasesInfo OpenMSInfo OpenPepXL OpenPepXLLF OpenSwathAnalyzer OpenSwathAssayGenerator OpenSwathChromatogramExtractor OpenSwathConfidenceScoring OpenSwathDIAPreScoring OpenSwathDecoyGenerator OpenSwathFeatureXMLToTSV OpenSwathFileSplitter OpenSwathMzMLFileCacher OpenSwathRTNormalizer OpenSwathRewriteToFeatureXML OpenSwathWorkflow PSMFeatureExtractor PeakPickerHiRes PeakPickerIterative PeakPickerWavelet PeptideIndexer PercolatorAdapter PhosphoScoring PrecursorMassCorrector ProteinInference ProteinQuantifier ProteinResolver QCCalculator QCEmbedder QCExporter QCExtractor QCImporter QCMerger QCShrinker QualityControl RNADigestor RNAMassCalculator RNPxlSearch RNPxlXICFilter SageAdapter SeedListGenerator SemanticValidator SequenceCoverageCalculator SimpleSearchEngine SiriusAdapter SpecLibCreator SpecLibSearcher SpectraFilterBernNorm SpectraFilterMarkerMower SpectraFilterNLargest SpectraFilterNormalizer SpectraFilterParentPeakMower SpectraFilterScaler SpectraFilterSqrtMower SpectraFilterThresholdMower SpectraFilterWindowMower SpectraMerger SpectraSTSearchAdapter StaticModification TICCalculator TOFCalibration TargetedFileConverter TextExporter TriqlerConverter XFDR XMLValidator XTandemAdapter OpenMS Suite for LC/MS data management and analyses 184684
openms
To update
UseGalaxy.be18 UseGalaxy.cz141 UseGalaxy.eu144 UseGalaxy.no124 UseGalaxy.or34
2.1.1+galaxy0 mz_to_sqlite Creates a SQLite database for proteomics data Proteomics Biological databases Conversion Peptide database search 3663
mztosqlite
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1.1.0 mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome 828
r-tidyverse
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2.0.0 msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling 4230
bioconductor-msstatstmt
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UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
4.0.0 msstats MSstats tool for analyzing mass spectrometry proteomic datasets Proteomics Proteomics experiment Protein expression Spectrum calculation Tag-based peptide identification Differential protein expression profiling 15777
bioconductor-msstats
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1.0.0 msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. 349
proteowizard
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0.5 msgfplus MSGF+ 2282
msgf_plus
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3.0.20287 msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container Proteomics Proteomics experiment Filtering Formatting 223468
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
0.1.19 mqppep_anova mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA 39
bioconductor-preprocesscore
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288 morpheus Morpheus MS Search Application Proteomics Peptide database search 3439
morpheus
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2.0.3 proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. 1944
moff
Up-to-date
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1.0.0 mgf_formatter 0
mgf-formatter
Up-to-date
2.0.2 metaquantome_db metaquantome_expand metaquantome_filter metaquantome_sample metaquantome_stat metaquantome_viz quantitative analysis of microbiome taxonomy and function Proteomics Metatranscriptomics Microbial ecology Proteomics experiment Metagenomics Principal component visualisation Visualisation Functional clustering Query and retrieval Differential protein expression analysis Heat map generation Quantification Indexing Filtering Statistical inference 14252
metaquantome
Up-to-date
UseGalaxy.be6 UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.fr6 UseGalaxy.no6 UseGalaxy.or6
1.9.4 metanovo Produce targeted databases for mass spectrometry analysis. Proteomics Microbial ecology Metagenomics Proteomics experiment Small molecules Target-Decoy de Novo sequencing Tag-based peptide identification Protein identification Expression analysis 14868
metanovo
Up-to-date
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1.0 metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage Genomics Model organisms Data submission, annotation and curation Sequence annotation 3594
metagene_annotator
Up-to-date
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2.0.0 meta_proteome_analyzer MetaProteomeAnalyzer 426
mpa-portable
Up-to-date
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2.0.3.0 maxquant maxquant_mqpar wrapper for MaxQuant Proteomics experiment Proteomics Statistics and probability Imputation Visualisation Protein quantification Statistical calculation Standardisation and normalisation Heat map generation Clustering Principal component plotting 43916
maxquant
Up-to-date
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0.2 map_peptides_to_bed Map peptides to a reference genome for display by a genome browser 112
biopython
To update
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1.22.0 maldi_quant_peak_detection maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. 9920
r-base
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0
To update
1.0 lfq_protein_quant Enable protein summarisation and quantitation 256
bioconductor-msnbase
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idconvert Convert mass spectrometry identification files on linux or MacOSX 671
proteowizard
To update
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2.30.1+galaxy1 hardklor kronik Hardklör 267
hardklor
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0.2.1 gffcompare_to_bed Filter and convert a gffCompare GTF to BED 10067
python
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20.0 fragpipe Data analysis for mass spectrometry-based proteomics. 630
fragpipe
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1.0.3.1 flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification Proteomics experiment Proteomics Label-free quantification 2549
flashlfq
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2.3 filter_by_fasta_ids Filter FASTA on the headers and/or the sequences 500125
python
To update
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0.11.0 feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy 54
msproteomicstools
Up-to-date
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1.0.2 fastg2protlib-peptides fastg2protlib-validate Generate FASTA from FASTG 87
To update
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1.2.0 fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together 232161
python
To update
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1.12.34 encyclopedia_encyclopedia encyclopedia_fasta_to_prosit_csv encyclopedia_library_to_blib encyclopedia_prosit_csv_to_library encyclopedia_quantify encyclopedia_searchtolib encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis 2571
encyclopedia
To update
UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.or4
2.1.8 eggnog_mapper eggnog_mapper_annotate eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences Metagenomics Phylogeny Transcriptomics Workflows Sequence analysis Homology-based gene prediction Genome annotation Fold recognition Information extraction Query and retrieval 385411
eggnog-mapper
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download eggnog data for eggnog-mapper 0
To update
downloads eggnog data for eggnog-mapper 0
To update
0
To update
0.1.0 digestdb 0
trans_proteomic_pipeline
To update
1.0.6 diffacto Diffacto comparative protein abundance estimation 33
diffacto
To update
UseGalaxy.cz1 UseGalaxy.eu1
0.3.5.0 diapysef diapysef is a convenience package for working with DIA-PASEF data 1755
diapysef
To update
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1.8.1 diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. 1053
To update
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1.2.0 dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. 120
bioconductor-dialignr
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2.1.3 dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics 540
dia_umpire
To update
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Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. 0
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0.3.4 dbbuilder Protein Database Downloader 23359
wget
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
3.4.3 cardinal_classification cardinal_colocalization cardinal_combine cardinal_data_exporter cardinal_filtering cardinal_mz_images cardinal_preprocessing cardinal_quality_report cardinal_segmentations cardinal_single_ion_segmentation cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets 152963
bioconductor-cardinal
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UseGalaxy.be9 UseGalaxy.cz11 UseGalaxy.eu11 UseGalaxy.fr11 UseGalaxy.no9 UseGalaxy.or9
3.0.13 calisp Calgary approach to isotopes in proteomics 669
calisp
To update
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3.0.21142 idpqonvertEmbedder idpassemble idpqonvert idpquery myrimatch 3399
bumbershoot
To update
UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.no5
2.6.0 blast_plus_remote_blastp NCBI BLAST+ with -remote option 0
blast
To update
UseGalaxy.fr1
0.2.0 bed_to_protein_map Converts a BED file to a tabular list of exon locations 2917
python
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
0.2.0 append_fdr 0
To update
1.3.4 thermo_raw_file_converter Thermo RAW file converter 11575
thermorawfileparser
To update
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vcfvcfintersect Intersect two VCF datasets 3215011
vcflib
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vcfsort Sort VCF dataset by coordinate 59796
vcflib
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vcfselectsamples Select samples from a VCF file 12503
vcflib
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vcfrandomsample Randomly sample sites from VCF dataset 1705
vcflib
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vcfprimers Extract flanking sequences for each VCF record 4082
vcflib
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vcfleftalign Left-align indels and complex variants in VCF dataset 4508
vcflib
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vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. 15754
vcflib
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vcfgenotypes Convert numerical representation of genotypes to allelic. 18027
vcflib
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vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles 11769
vcflib
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vcfflatten2 Removes multi-allelic sites by picking the most common alternate 3218
vcflib
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vcffixup Count the allele frequencies across alleles present in each record in the VCF file. 13550
vcflib
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vcffilter2 Tool for filtering VCF files 457815
vcflib
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vcfdistance Calculate distance to the nearest variant. 9059
vcflib
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vcfcommonsamples Output records belonging to samples commong between two datasets. 3761
vcflib
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vcfcombine Combine multiple VCF datasets 36242
vcflib
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vcfcheck Verify that the reference allele matches the reference genome 9153
vcflib
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vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 20855
vcflib
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vcfbedintersect Intersect VCF and BED datasets 42486
vcflib
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vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. 3980
vcflib
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vcfannotate Intersect VCF records with BED annotations 32514
vcflib
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vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines 65319
vcflib
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vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. 25232
vcflib
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vcf2tsv Converts VCF files into tab-delimited format 601904
vcflib
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snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome 3088
snpsift
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snpSift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani 1428
snpsift
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snpSift_annotate snpSift_caseControl snpSift_extractFields snpSift_filter snpSift_int snpSift_rmInfo snpsift_vartype snpSift_vcfCheck snpEff SnpSift tools from Pablo Cingolani 17018898
snpsift
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5.2 snpEff snpEff_build_gb snpEff_databases snpEff_download snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox 843282
biopython
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1.20 0
samtools
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2.1.3 kraken2 Kraken2 for taxonomic designation. Taxonomy Metagenomics Taxonomic classification 1852919
kraken2
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kraken-filter kraken-mpa-report kraken-report kraken-translate kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. Taxonomy Metagenomics Taxonomic classification 534264
kraken
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1.1.5 tabular_to_fastq Tabular to FASTQ converter 85662
galaxy_sequence_utils
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1.1.5 fastq_to_fasta_python FASTQ to FASTA converter 1335031
galaxy_sequence_utils
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1.1.5 fastq_trimmer FASTQ Trimmer by quality 180242
galaxy_sequence_utils
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1.1.5 fastq_to_tabular FASTQ to Tabular converter 131909
galaxy_sequence_utils
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1.1.5 fastq_stats FASTQ Summary Statistics by column 135544
galaxy_sequence_utils
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1.1.5 fastq_paired_end_splitter FASTQ splitter on joined paired end reads 111380
galaxy_sequence_utils
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1.1.5 fastq_paired_end_joiner FASTQ joiner on paired end reads 163487
galaxy_sequence_utils
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1.1.5 fastq_paired_end_interlacer FASTQ interlacer on paired end reads 158289
galaxy_sequence_utils
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1.1.5 fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. 80739
galaxy_sequence_utils
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1.1.5 fastq_masker_by_quality FASTQ Masker by quality score 14594
galaxy_sequence_utils
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1.1.5 fastq_manipulation Manipulate FASTQ reads on various attributes. 46640
galaxy_sequence_utils
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1.1.5 fastq_groomer Convert between various FASTQ quality formats. 1633662
galaxy_sequence_utils
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1.1.5 fastq_filter Filter FASTQ reads by quality score and length 273963
galaxy_sequence_utils
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1.1.5 fastq_combiner Combine FASTA and QUAL into FASTQ 214033
galaxy_sequence_utils
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0.0.14 cshl_fastx_trimmer Trim sequences 524758
fastx_toolkit
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UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
0.0.14 cshl_fastx_reverse_complement Reverse-Complement 155610
fastx_toolkit
Up-to-date
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
0.0.14 cshl_fastx_renamer Rename sequences 46871
fastx_toolkit
Up-to-date
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
0.0.14 cshl_fastx_quality_statistics Compute quality statistics 129051
fastx_toolkit
Up-to-date
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
0.0.14 cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart 38299
fastx_toolkit
Up-to-date
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
0.0.14 cshl_fastx_collapser Collapse sequences 639227
fastx_toolkit
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0.0.14 cshl_fastx_clipper Clip adapter sequences 157341
fastx_toolkit
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0.0.14 cshl_fastx_barcode_splitter Barcode Splitter 259007
fastx_toolkit
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0.0.14 cshl_fastx_artifacts_filter Remove sequencing artifacts 45519
fastx_toolkit
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0.0.14 cshl_fastq_to_fasta FASTQ to FASTA converter 370165
fastx_toolkit
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0.0.14 cshl_fastq_quality_filter Filter by quality 372308
fastx_toolkit
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0.0.14 cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) 17187
fastx_toolkit
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0.0.14 cshl_fastq_quality_boxplot Draw quality score boxplot 89226
fastx_toolkit
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0.0.14 cshl_fasta_nucleotides_changer RNA/DNA converter. 12868
fastx_toolkit
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0.0.14 cshl_fasta_formatter FASTA Width formatter 71033
fastx_toolkit
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0.0.14 cshl_fasta_clipping_histogram Length Distribution chart 16858
fastx_toolkit
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2.2.1 cuffquant The Cuffquant tool 21661
cufflinks
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2.2.1 cuffnorm The Cuffnorm tool 17464
cufflinks
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2.2.1 cuffmerge Galaxy wrappers for the Cuffmerge tool. 119646
cufflinks
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2.2.1 cufflinks Galaxy wrappers for the Cufflinks tool. 592195
cufflinks
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2.2.1 cuffdiff Galaxy wrappers for the Cuffdiff tool. 180650
cufflinks
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2.2.1 cuffcompare Galaxy wrappers for the Cuffcompare tool. 33782
cufflinks
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1.4.5 bacteria_tradis tradis_essentiality tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. Mobile genetic elements Workflows Sequence analysis 19395
biotradis
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2.5.2 bamtools_split_mapped bamtools_split_paired bamtools_split_ref bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. Sequencing Data management Sequence analysis Data handling Sequence alignment analysis 76980
bamtools
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2.5.2 bamFilter Filter BAM datasets on various attributes using bamtools filter Sequencing Data management Sequence analysis Data handling Sequence alignment analysis 748591
bamtools
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2.5.2 bamtools Operate on and transform BAM datasets in various ways using bamtools Sequencing Data management Sequence analysis Data handling Sequence alignment analysis 268010
bamtools
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1.0 zerone ChIP-seq discretization and quality control 222
zerone
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1.2a.2 yahs Yet Another Hi-C scaffolding tool 5787
yahs
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xpath XPath XML querying tool 435
perl-xml-xpath
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2.03 winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. 1119
winnowmap
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1.0 windowmasker_mkcounts windowmasker_ustat Identify repetitive regions using WindowMasker 5706
blast
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3.5.0 rgweblogo3 Sequence Logo generator for fasta Nucleic acid sites, features and motifs Sequence analysis Sequence cluster visualisation Sequence visualisation Sequence motif recognition 62379
weblogo
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0.1.2 simple_weather provides simple weather in text format 0
curl
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3.0.6 vsnp_add_zero_coverage vsnp_build_tables vsnp_determine_ref_from_data vsnp_get_snps vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. 0
pysam
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2.8.3 vsearch_alignment vsearch_chimera_detection vsearch_clustering vsearch_dereplication vsearch_masking vsearch_search vsearch_shuffling vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. Metagenomics Sequence analysis DNA mapping Chimera detection 137304
vsearch
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0.0.7 volcanoplot Tool to create a Volcano Plot 324849
r-ggplot2
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1.0.0 virhunter Deep Learning method for novel virus detection in sequencing data Virology Sequence classification 2280
numpy
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0.7.1 virheat generates a heatmap of allele frequencies from vcf files 45
virheat
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1.1.0+galaxy0 virannot_blast2tsv virannot_otu virAnnot_rps2tsv virAnnot wrappers Metagenomics Virology Microbial ecology Sequence annotation Sequence clustering Sequence cluster visualisation 855
biopython
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vg
1.23.0 vg_convert vg_deconstruct vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods 1437
vg
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1.3.1 verkko Telomere-to-telomere assembly pipeline 390
verkko
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2.2.6+galaxy2 velvetoptimiser Automatically optimize Velvet assemblies Genomics Sequence assembly Optimisation and refinement Sequence assembly 58019
velvet
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velvetg velveth de novo genomic assembler specially designed for short read sequencing technologies Sequence assembly Formatting De-novo assembly 333257
velvet
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0.17.17 velocyto_cli Velocyto is a library for the analysis of RNA velocity. RNA-Seq analysis Splicing analysis 705
velocyto.py
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2.4-3 vegan_diversity vegan_fisher_alpha vegan_rarefaction an R package fo community ecologist Ecology Phylogenetics Environmental science Standardisation and normalisation Analysis 19671
r-vegan
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0.3.5 vcfanno Annotate VCF files Genetic variation Data submission, annotation and curation SNP annotation 3561
vcfanno
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1.6.21 vcf2maf vcf2maf: Convert VCF into MAF 4494
vcf2maf
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1.2.2 varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses Virology Probes and primers PCR primer design 1314
varvamp
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2.4.3 varscan_copynumber varscan_mpileup varscan_somatic VarScan is a variant caller for high-throughput sequencing data 96009
varscan
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2.0.0 mut2read mut2sscs read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data 1896
matplotlib
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1.8.3 vardict_java VarDict - calls SNVs and indels for tumour-normal pairs 1161
python
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1.0.2 vapor Classify Influenza samples from raw short read sequence data Whole genome sequencing Mapping Sequence assembly Data retrieval De-novo assembly Read mapping 217617
vapor
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valet A pipeline for detecting mis-assemblies in metagenomic assemblies. Metagenomics Sequence assembly Sequence assembly Sequence assembly visualisation 2392
valet
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0.2.1 usher_matutils usher UShER toolkit wrappers Phylogeny Evolutionary biology Cladistics Genotype and phenotype Phylogenomics Classification Phylogenetic tree visualisation Phylogenetic inference (from molecular sequences) 3180
usher
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0.5.1 unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. Microbiology Genomics Sequencing Sequence assembly Genome assembly Aggregation 522849
unicycler
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1.1.6 umi_tools_count umi_tools_dedup umi_tools_extract umi_tools_group umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq NGS Sequence sites, features and motifs Quality affairs Sequencing quality control 259890
umi_tools
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472 ucsc_wigtobigwig converts bedGraph (wig) files into binary bigwig Sequence analysis 26634
ucsc-wigtobigwig
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469 ucsc_nettoaxt Convert net (and chain) to axt format. Sequence analysis 24
ucsc-nettoaxt
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469 ucsc_netsyntenic Add synteny info to a net dataset Sequence analysis 69
ucsc-netsyntenic
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UseGalaxy.or1
469 ucsc_netfilter Filter out parts of net Sequence analysis 27
ucsc-netfilter
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469 ucsc_chainsort Sort chains. By default sorts by score. Sequence analysis 39
ucsc-chainsort
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UseGalaxy.or1
469 ucsc_chainprenet Remove chains that don't have a chance of being netted Sequence analysis 39
ucsc-chainprenet
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469 ucsc_chainnet Make alignment nets out of chains Sequence analysis 42
ucsc-chainnet
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469 ucsc_chainantirepeat Remove repeated chains Sequence analysis 0
ucsc-chainantirepeat
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469 ucsc_axtomaf Convert dataset from axt to MAF format. Sequence analysis 36
ucsc-axttomaf
Up-to-date
UseGalaxy.or1
469 ucsc_axtchain Chain together genome alignments Sequence analysis 33
ucsc-axtchain
Up-to-date
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472 ucsc-twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA Sequence analysis 4078
ucsc-twobittofa
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469 maftoaxt Convert dataset from MAF to axt format Sequence analysis 27
ucsc-maftoaxt
Up-to-date
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473 fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs Sequence analysis 4053
ucsc-fatovcf
Up-to-date
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469 fasplit faSplit is a tool to split a single FASTA file into several files Sequence analysis 35546
ucsc-fasplit
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472 ucsc_blat Standalone blat sequence search command line tool Sequence analysis Sequence alignment 0
ucsc-blat
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1.30.0 tximport Wrapper for the Bioconductor package tximport Transcriptomics Gene transcripts Workflows Pathway or network analysis Formatting RNA-Seq analysis 28380
bioconductor-tximport
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0.0.2 tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation 1734
r-rtsne
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1.1.2.5 tsebra This tool has been developed to combine BRAKER predictions. Gene expression RNA-Seq Gene transcripts Model organisms Homology-based gene prediction Alternative splicing prediction 129
tsebra
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0.5.5 trycycler_cluster trycycler_consensus trycycler_partition trycycler_reconcile_msa trycycler_subsample Trycycler toolkit wrappers Sequence assembly DNA Human biology Whole genome sequencing Genomics Genome assembly Sequence trimming Scaffold gap completion Sequence assembly validation 60225
trycycler
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3.2.2 trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. Gene expression Transcriptomics Gene functional annotation 15592
trinotate
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2.15.1 trinity_abundance_estimates_to_matrix trinity_align_and_estimate_abundance trinity_analyze_diff_expr trinity_contig_exn50_statistic trinity_define_clusters_by_cutting_tree describe_samples trinity_filter_low_expr_transcripts trinity_gene_to_trans_map trinity_run_de_analysis trinity_samples_qccheck trinity_super_transcripts trinity trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq Transcriptomics Gene expression Gene transcripts Transcriptome assembly 345015
trinity
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0.39 trimmomatic A flexible read trimming tool for Illumina NGS data 3988590
trimmomatic
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1.5.0 trimal Tool for automated alignment trimming Sequence analysis Sequencing Sequence sites, features and motifs Multiple sequence alignment 3216
trimal
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transtermhp Finds rho-independent transcription terminators in bacterial genomes Transcription factors and regulatory sites Transcriptional regulatory element prediction 1932
transtermhp
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3.0.2 gff_to_prot transit_gumbel transit_hmm transit_resampling transit_tn5gaps TRANSIT DNA Sequencing Mobile genetic elements Transposon prediction 13881
transit
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5.5.0 transdecoder TransDecoder finds coding regions within transcripts Genomics Gene transcripts RNA-Seq Gene expression Sequence assembly Whole genome sequencing Coding region prediction de Novo sequencing De-novo assembly 49604
transdecoder
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0.7.8 tracy_align tracy_assemble tracy_basecall tracy_decompose A suite tools for basecalling, alignment, assembly and deconvolution of Sanger chromatograms using tracy. 10947
tracy
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0.1.4 tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. 156
tracegroomer
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0.9.2 tooldistillator tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files Microbiology Bioinformatics Sequence analysis Data handling Parsing 23697
tooldistillator
Up-to-date
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1.0.14 tn93_readreduce tn93 tn93_cluster tn93_filter Compute distances between sequences 13590
tn93
Up-to-date
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1.1 tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. 816
tetyper
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2.2.3 tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. 3738
tetranscripts
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1.0.3 telescope_assign Single locus resolution of Transposable ELEment expression. RNA-Seq Transcriptomics Mapping Gene transcripts Sequence assembly Essential dynamics Sequence trimming RNA-Seq quantification Expression analysis Read mapping 0
telescope
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1.0.1 te_finder Transposable element insertions finder Sequencing Mobile genetic elements Workflows Evolutionary biology Genetic variation Genome indexing Variant calling PCR primer design 627
samtools
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1.0.1 tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) 49016
tbvcfreport
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1.2 tbl2gff3 Table to GFF3 9585
bcbiogff
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0.4.0 tb_variant_filter M. tuberculosis H37Rv VCF filter 196497
tb_variant_filter
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6.4.0 tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. Antimicrobial resistance prediction 82851
delly
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0.7.0 taxpasta standardise taxonomic profiles Taxonomy Metagenomics Standardisation and normalisation Aggregation Formatting Conversion 270
taxpasta
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2.7.1+galaxy0 taxonomy_krona_chart Krona pie chart from taxonomic profile Metagenomics Visualisation 244625
krona
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0.3.0 taxonomy_filter_refseq Filter RefSeq by taxonomy 0
rust-ncbitaxonomy
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0.20.0 name2taxid profile2cami TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit Taxonomy Biotechnology Ecology Formatting Data retrieval 1230
taxonkit
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1.0.7 tasmanian_mismatch Analysis of positional mismatches 828
tasmanian-mismatch
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1.0.2 tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. 2664
openjdk
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1.2.4 table_compute Perform general-purpose table operations 768609
pandas
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1.7.1 syri Synteny and Rearrangement Identifier DNA polymorphism Sequence assembly DNA structural variation Mapping Sequencing Haplotype mapping Variant calling Genotyping Sequence assembly Read mapping 21
syri
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1.0 syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. 90
clustalo
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1.0 swiftlink Parallel MCMC Linkage Analysis 0
swiftlink
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0.6.94 structureharvester for parsing STRUCTURE outputs and for performing the Evanno method 0
structureharvester
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2.3.4 structure for using multi-locus genotype data to investigate population structure. Population genetics Genetic variation analysis 11052
structure
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2.2.3 stringtie stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. Transcriptomics RNA-Seq Transcriptome assembly RNA-Seq analysis 1725150
stringtie
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2.9.10 strelka_germline strelka_somatic Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision. 7779
strelka
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3.2.2 straindesign_analyzing_model straindesign_reduce_model straindesign_simulate_deletion Toolbox to optimize biological model 0
straindesign
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0.11.0 staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Microbiology Public health and epidemiology Infectious disease Antimicrobial resistance prediction 152867
staramr
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0.5.4-3+galaxy1 star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR 11973
star-fusion
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2.55 stacks2_clonefilter stacks2_cstacks stacks2_denovomap stacks2_gstacks stacks2_kmerfilter stacks2_populations stacks2_procrad stacks2_refmap stacks2_shortreads stacks2_sstacks stacks2_tsv2bam stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq 86331
stacks
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stacks_assembleperead stacks_clonefilter stacks_cstacks stacks_denovomap stacks_genotypes stacks_populations stacks_procrad stacks_pstacks stacks_refmap stacks_rxstacks stacks_sstacks stacks_stats stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq Mapping Population genetics Data handling 42386
stacks
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0.2.0 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens Whole genome sequencing Public health and epidemiology Comparative genomics Multilocus sequence typing 1161
samtools
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3.1.1 fasterq_dump fastq_dump sam_dump NCBI Sequence Read Archive toolkit utilities DNA Genomics Sequencing Data handling 3282472
sra-tools
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1.0.13 squirrel_phylo squirrel_qc QC and Phylogenetic analysis of MPXV Virology Phylogenetic analysis Sequencing quality control 0
squirrel
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0.1.2 spyboat Wavelet analysis for 3d-image stacks 462
spyboat
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2.1 spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads Microbiology Sequencing Sequence composition, complexity and repeats Genetic variation Variant pattern analysis 5652
spotyping
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0.1.5 spapros_evaluation spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Primer and probe design Visualisation 9
spapros
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2.4.9 list_spaln_tables spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. 14543
python
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4.1.0 spades_biosyntheticspades spades_coronaspades spades_metaplasmidspades metaspades spades_metaviralspades spades_plasmidspades rnaspades spades_rnaviralspades spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. Sequence assembly Genome assembly 879651
spades
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2.2.1 spacexr_cside spacexr_rctd Cell type identification and cell type-specific differential expression in spatial transcriptomics 0
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20210201 sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Whole genome sequencing Genotype and phenotype Genetic variation Metagenomics Antimicrobial resistance prediction Variant calling Genotyping 3
sonneityping
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2.1.7 socru Order and orientation of complete bacterial genomes 2774
socru
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1.0 snpfreqplot A plotting app to visualise the SNPs across a region 20334
r-base
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snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox DNA polymorphism Genetic variation Nucleic acid sites, features and motifs SNP detection 2695614
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2.5.1 snp_sites Finds SNP sites from a multi-FASTA alignment file 34287
snp-sites
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0.8.2 snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment 46067
snp-dists
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snippy_core snippy snippy_clean_full_aln Contains the snippy tool for characterising microbial snps Genomics Model organisms DNA polymorphism Phylogenetics Phylogenetic tree visualisation Phylogenetic tree generation Variant calling 922052
snippy
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1.6 snipit Summarise snps relative to a reference sequence Virology Base position variability plotting 3117
snipit
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2.5.2 sniffles Galaxy wrapper for sniffles DNA structural variation Sequencing Sequence analysis Structural variation detection 15420
sniffles
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2.6.4 snapatac2_clustering snapatac2_peaks_and_motif snapatac2_plotting snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis Epigenomics Cell biology Chromosome conformation capture Mapping Sequencing Essential dynamics Dimensionality reduction Gene expression profiling 8523
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2013_11_29 snap snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. DNA DNA polymorphism Genetics Gene prediction 8746
snap
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0.2.5 smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing Sequence assembly Genetic variation Mathematics Sequence trimming Genotyping k-mer counting 5280
smudgeplot
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0.5.1 smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. Genomics Population genetics Workflows Virology Sequencing Read pre-processing Sequence alignment Genetic variation analysis 477
smallgenomeutilities
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0.30.1 sleuth Sleuth is a program for differential analysis of RNA-Seq data. RNA-Seq Gene expression Statistics and probability Expression data visualisation Differential gene expression analysis Gene expression profiling Statistical calculation 543
r-sleuth
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0.4.3 alleyoop slamdunk Slamdunk maps and quantifies SLAMseq reads 4342
slamdunk
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0.10.1 sinto_barcode sinto_fragments Sinto single-cell analysis tools Bioinformatics Cell biology 1899
sinto
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1.7.2 sina SINA reference based multiple sequence alignment Sequencing RNA Nucleic acid structure analysis Taxonomy Sequence analysis Taxonomy Sequence alignment analysis Multiple sequence alignment Taxonomic classification Structure-based sequence alignment 11568
sina
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0.0.2 abstracts_by_pmids pmids_to_pubtator_matrix pubmed_by_queries text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. 2202
r-argparse
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1.33.3 sickle A windowed adaptive trimming tool for FASTQ files using quality Data quality management Sequence trimming 93437
sickle-trim
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1.1.0 shovill Faster de novo assembly pipeline based around Spades Genomics Microbiology Sequence assembly Genome assembly 391481
shovill
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1.1.3 shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode Metagenomics Sequencing Genetics Haplotype mapping Variant calling 0
shorah
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0.6.0 shasta Fast de novo assembly of long read sequencing data 5430
shasta
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2.2.0 sfold Predict the probable RNA secondary structures through structure ensemble sampling 0
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5.0 seurat_create seurat_data seurat_integrate seurat_clustering seurat_preprocessing seurat_plot seurat_reduce_dimension Seurat - R toolkit for single cell genomics RNA-Seq Transcriptomics 8901
r-seurat
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0.7.5 seqwish Alignment to variation graph inducer 813
seqwish
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0.12.0 sequali Fast sequencing data quality metrics for short and long reads Data quality management Sequence analysis Sequencing quality control Statistical calculation 0
sequali
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1.4 seqtk_comp seqtk_cutN seqtk_dropse seqtk_fqchk seqtk_hety seqtk_listhet seqtk_mergefa seqtk_mergepe seqtk_mutfa seqtk_randbase seqtk_sample seqtk_seq seqtk_subseq seqtk_telo seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats Data management Data handling Sequence file editing 1291009
seqtk
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1.3.1 seqsero2 Salmonella serotype prediction from genome sequencing data Whole genome sequencing Sequence assembly Genomics Genome indexing Antimicrobial resistance prediction Genome alignment 39402
seqsero2
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1.3.2 seqprep Tool for merging paired-end Illumina reads and trimming adapters. Genomics Sequence assembly Sequencing Probes and primers Nucleic acid design 8226
seqprep
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2.10.0 seqkit_fx2tab seqkit_head seqkit_locate seqkit_sort seqkit_stats seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation Database management Sequence analysis DNA transcription Sequence trimming DNA translation Sequence conversion 30258
seqkit
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0.1.2 seqcomplexity Sequence complexity for raw reads 606
seqcomplexity
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2.3 seq2hla Precision HLA typing and expression from RNAseq data Transcriptomics Mapping Read mapping Genetic variation analysis 1299
seq2hla
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2.0.2 semibin_bin semibin_concatenate_fasta semibin_generate_cannot_links semibin_generate_sequence_features semibin semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks Metagenomics Machine learning Microbial ecology Sequence assembly Sequence assembly Read binning 5742
semibin
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0.3.0 selenzy_wrapper Performs enzyme selection from a reaction query. 0
selenzy_wrapper
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1.3 seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. 39954
seacr
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1.0.0+galaxy2 scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data Gene expression RNA-Seq Sequencing Genome annotation Validation Alignment Visualisation 3501
bioconductor-scpipe
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1.6.16 scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. Genotype and phenotype Model organisms GWAS study Functional genomics Analysis 3360
scoary
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0.4.2 scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics 5022
scikit-bio
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4 schicexplorer_schicadjustmatrix schicexplorer_schiccluster schicexplorer_schicclustercompartments schicexplorer_schicclusterminhash schicexplorer_schicclustersvl schicexplorer_schicconsensusmatrices schicexplorer_schiccorrectmatrices schicexplorer_schiccreatebulkmatrix schicexplorer_schicdemultiplex schicexplorer_schicinfo schicexplorer_schicmergematrixbins schicexplorer_schicmergetoscool schicexplorer_schicnormalize schicexplorer_schicplotclusterprofiles schicexplorer_schicplotconsensusmatrices schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. Workflows DNA Chromosome conformation capture ChIP-seq Epigenetics Validation Visualisation Standardisation and normalisation 4523
schicexplorer
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0.0.7 sceasy_convert Converter between difference single-cell formats Data handling 5990
r-sceasy
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1.22.0 scater_create_qcmetric_ready_sce scater_filter scater_plot_dist_scatter scater_plot_pca scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. RNA-Seq Quality affairs Molecular genetics Read pre-processing Sequencing quality control Sequence visualisation 7015
bioconductor-scater
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1.10.2 scanpy_cluster_reduce_dimension scanpy_filter scanpy_inspect scanpy_normalize scanpy_plot scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python Gene expression Cell biology Genetics Single-cell sequencing Differential gene expression analysis 367416
scanpy
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0.1.13 sbml2sbol Convert SBML to SBOL format 0
sbml2sbol
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0.1 sarscov2summary sarscov2summary custom script 1179
sarscov2summary
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1.0 sarscov2formatter sarscov2formatter custom script 1722
sarscov2formatter
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0.2.2 sansa_annotate Sansa is a tool for structural variant annotation. 417
sansa
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0.1.26 samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files DNA Sequencing Mapping Split read mapping 0
samblaster
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2.3 salsa A tool to scaffold long read assemblies with Hi-C Sequence assembly DNA binding sites Mapping Genome assembly De-novo assembly Scaffolding 5802
salsa2
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1.26.0 ruvseq Remove Unwanted Variation from RNA-Seq Data Gene expression RNA-seq Differential gene expression analysis 10909
bioconductor-ruvseq
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5.0.3 rseqc_FPKM_count rseqc_RNA_fragment_size rseqc_RPKM_saturation rseqc_bam2wig rseqc_bam_stat rseqc_clipping_profile rseqc_deletion_profile rseqc_geneBody_coverage rseqc_geneBody_coverage2 rseqc_infer_experiment rseqc_inner_distance rseqc_insertion_profile rseqc_junction_annotation rseqc_junction_saturation rseqc_mismatch_profile rseqc_read_GC rseqc_read_NVC rseqc_read_distribution rseqc_read_duplication rseqc_read_hexamer rseqc_read_quality rseqc_tin an RNA-seq quality control package Sequencing Data handling 1137781
rseqc
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2.7.0 rrparser Reaction Rules Parser 0
rrparser
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5.13.1 rptools_rpextractsink rptools_rpfba rptools_rpranker rptools_rpreport rptools_rpviz Suite of tools that work on rpSBML format 0
rptools
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5.12.3 rpfba Perform FBA for the RetroPath2.0 heterologous pathways 0
rptools
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1.2.2 rpbasicdesign Extracting enzyme IDs from rpSBML files 0
rpbasicdesign
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1.5.1 rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 0
rp2paths
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3.2.1 rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output 0
rp2biosensor
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3.13.0 roary Roary the pangenome pipeline DNA Genomics Mapping Genome assembly 110649
roary
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2.3.0 rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. Sequence assembly Transcriptomics RNA-Seq De-novo assembly Transcriptome assembly Sequence assembly validation 7248
rnaquast
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1.2.0 ribowaltz_process ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data Computational biology 582
ribowaltz
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2.7.11a rna_star rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper RNA-Seq Transcriptomics Sequence alignment 2792811
star
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3.0.2 rgcca multi-block analysis 393
rgccacmd
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0.1.8 revoluzer_crex revoluzer_distmat revoluzer wrappers Molecular evolution Phylogeny Structural variation detection 9138
revoluzer
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1.0.2 resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. 597
python
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1.4.2 cast melt Flexibly restructure and aggregate data using just the two functions melt and dcast 12313
r-reshape2
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repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. 1430
matplotlib
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2.0.5 repeatmodeler RepeatModeler - Model repetitive DNA Sequence composition, complexity and repeats Sequence composition, complexity and repeats Repeat sequence detection 57969
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4.1.5 repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. Sequence analysis Sequence composition, complexity and repeats Genome annotation 64172
repeatmasker
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red
2018.09.10 red Red (REpeat Detector) RNA Sequencing Data visualisation RNA-Seq analysis Editing 5781
red
red
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1.16.1 recentrifuge "With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." Metagenomics Microbial ecology Metagenomic sequencing Taxonomic classification Expression analysis Cross-assembly 7431
recentrifuge
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0.2.2 read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads Pathology Genomics Filtering Genome alignment 11355
read-it-and-keep
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1.0.3+galaxy1 rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. RNA RNA-Seq Sequencing Sequencing error detection 2337
rcorrector
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8.2.12 raxml RAxML - A Maximum Likelihood based phylogenetic inference Phylogenetics Sequence analysis Sequence analysis Phylogenetic tree analysis 90367
raxml
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1.8.3 raven Raven is a de novo genome assembler for long uncorrected reads. Sequence assembly Whole genome sequencing Genomics De-novo assembly Genome assembly Read pre-processing 70506
raven-assembler
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2.0.0 rasusa Randomly subsample sequencing reads to a specified coverage Genomics Sequence analysis Sequence assembly Sequencing RNA-Seq Sequence assembly validation Sequencing quality control 213
rasusa
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2.3.2 rapidnj Galaxy wrapper for the RapidNJ tool Phylogeny Phylogenetic tree generation 15300
rapidnj
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2.1.0 ragtag Reference-guided scaffolding of draft genomes tool. Sequence assembly Genome assembly 18783
ragtag
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0.2.3 raceid_clustering raceid_filtnormconf raceid_inspectclusters raceid_inspecttrajectory raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis Cell biology Molecular interactions, pathways and networks RNA-Seq Gene expression Expression profile clustering Expression analysis Molecular dynamics 24619
r-raceid
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2.5 quicktree neighbour-joining phylogenetic inference Phylogenetics Phylogenetic inference (from molecular sequences) 195
quicktree
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0.3 quickmerge Merge long-read and hybrid assemblies to increase contiguity Structural variation Sequence assembly DNA polymorphism Whole genome sequencing Genotype and phenotype Genome assembly Scaffolding De-novo assembly Genotyping 0
quickmerge
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3.3.1 filter_tabular query_tabular sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output 494472
python
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0.9.0 query_impc Contains a tool to query the IMPC database. 12
requests
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5.3.0 quast Quast (Quality ASsessment Tool) evaluates genome assemblies. Sequence assembly Visualisation Sequence assembly validation 623276
quast
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2.3 qualimap_bamqc qualimap_counts qualimap_multi_bamqc qualimap_rnaseq Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. Data quality management Sequencing quality control 2572866
qualimap
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0.1.0 qq_manhattan 48
r-qqman
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0.1.0 qiime_extract_viz Extract vizualization from QIIME artifacts 312
unzip
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qiime_align_seqs qiime_alpha_diversity qiime_alpha_rarefaction qiime_assign_taxonomy qiime_beta_diversity qiime_beta_diversity_through_plots qiime_compare_categories qiime_core_diversity qiime_count_seqs qiime_extract_barcodes qiime_filter_alignment qiime_filter_fasta qiime_filter_otus_from_otu_table qiime_filter_samples_from_otu_table qiime_filter_taxa_from_otu_table qiime_jackknifed_beta_diversity qiime_make_emperor qiime_make_otu_heatmap qiime_make_phylogeny qiime_multiple_join_paired_ends qiime_multiple_split_libraries_fastq qiime_pick_closed_reference_otus qiime_pick_open_reference_otus qiime_pick_otus qiime_pick_rep_set qiime_plot_taxa_summary qiime_split_libraries qiime_split_libraries_fastq qiime_summarize_taxa qiime_summarize_taxa_through_plots qiime_upgma_cluster qiime_validate_mapping_file QIIME to perform microbial community analysis Microbial ecology Phylogeny Metagenomics Metatranscriptomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 124305
qiime
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qiime_collapse_samples qiime_make_otu_table QIIME to perform microbial community analysis Microbial ecology Phylogeny Metagenomics Metatranscriptomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 6723
qiime
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1.0.0+galaxy1 qfilt Filter sequencing data 0
qfilt
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1.4.2 pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. Sequencing Gene transcripts Bioinformatics Deposition Data retrieval 525
pysradb
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3.8 pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. Model organisms Imaging Workflows Visualisation Formatting 83505
pygenometracks
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5.0.2 pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. 9369
pyega3
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2.5.2 pycoqc QC metrics for ONT Basecalling Sequence analysis Data quality management Sequencing Sequencing quality control Statistical calculation 81324
pycoqc
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1.2.6 purge_dups Purge haplotigs and overlaps in an assembly based on read depth Sequence assembly Genome assembly Read binning Scaffolding 66966
purge_dups
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1.0.4 pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data 4155
pureclip
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1.0.3 psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. Sequence assembly Transcriptome assembly 78
psiclass
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6.3.5 proteinortho proteinortho_grab_proteins proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. Comparative genomics Sequence clustering Sequence analysis 12942
proteinortho
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0.1.6 prot_scriber Protein annotation of short human readable descriptions 36
prot-scriber
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1.14.6 prokka Rapid annotation of prokaryotic genomes Genomics Model organisms Virology Gene prediction Coding region prediction Genome annotation 3277782
prokka
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progressivemauve xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner 16755
progressivemauve
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2.6.3 prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes Genomics Sequence analysis Genome annotation 12309
prodigal
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@TOOL_VERSION+galaxy2 prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets Transcriptomics Metagenomics Genomics Read pre-processing Sequence trimming Sequence contamination filtering 70824
prinseq
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0.0.7 pretext_graph pretext_map pretext_snapshot Process genome contacts maps processing images. 25959
pretextgraph
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0.6.2 presto_alignsets presto_assemblepairs presto_buildconsensus presto_collapseseq presto_filterseq presto_maskprimers presto_pairseq presto_parseheaders presto_parselog presto_partition prestor_abseq3 pRESTO toolkit for immune repertoire analysis. Sequencing DNA Immunology Nucleic acid sequence analysis 213361
presto
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2.2.2 ppanggolin_all ppanggolin_msa Microbial Partitioned PanGenome Metagenomics Gene and protein families Model organisms Public health and epidemiology Mapping Rarefaction Essential dynamics Sequence assembly Genome annotation 0
ppanggolin
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0.6.1a1 poretools_events poretools_extract poretools_hist poretools_nucdist poretools_occupancy poretools_qualdist poretools_qualpos poretools_squiggle poretools_stats poretools_tabular poretools_times poretools_winner poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. DNA Sequencing Nucleic acid sequence analysis 198248
poretools
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porechop Porechop - Finding and removing adapters from Oxford Nanopore reads 1444141
porechop
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0.6.0 polypolish "Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix." Sequence assembly Sequence composition, complexity and repeats Mapping Genome assembly Read mapping Mapping assembly Sequencing error detection 3726
polypolish
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1.90b6.21 plink Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. GWAS study Genetic variation analysis 5595
plink
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2.1.6 plasmidfinder "PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage" Whole genome sequencing Sequence assembly Mapping Probes and primers Genome assembly Scaffolding Multilocus sequence typing 97866
plasmidfinder
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1.1.0 PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. Metagenomics Sequence assembly Mobile genetic elements Machine learning Sequence analysis 185318
plasflow
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0.37.3.1 pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. 5806
pizzly
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0.2 pipelign Multipe sequence alignment 32662
pipelign
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1.20.1 pilon pilon is a tool for assembly improvement and variant analysis in bacteria Assembly Sequence assembly Analysis Read alignment 67942
pilon
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2.5.3 picrust2_add_descriptions picrust2_hsp picrust2_metagenome_pipeline picrust2_pathway_pipeline picrust2_pipeline picrust2_place_seqs picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States Metagenomics Microbiology Phylogenetics Metagenomic sequencing Phylogenetic reconstruction Expression analysis Rarefaction Pathway analysis 16284
picrust2
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1.1.1 picrust_categorize picrust_compare_biom picrust_format_tree_and_trait_table picrust_metagenome_contributions picrust_normalize_by_copy_number picrust_predict_metagenomes PICRUSt wrappers Metagenomics Microbial ecology Functional, regulatory and non-coding RNA Metagenomic sequencing Phylogenetic reconstruction Expression analysis Genome annotation DNA barcoding 10907
picrust
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0.2.0 pick_value Compose a text parameter value using text, integer and float values 29880
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3.1.1 picard_AddCommentsToBam picard_AddOrReplaceReadGroups picard_BedToIntervalList picard_CleanSam picard_CASM picard_CollectBaseDistributionByCycle picard_CollectGcBiasMetrics picard_CollectHsMetrics picard_CollectInsertSizeMetrics picard_CollectRnaSeqMetrics picard_artifact_metrics picard_CollectWgsMetrics picard_DownsampleSam picard_EstimateLibraryComplexity picard_FastqToSam picard_FilterSamReads picard_FixMateInformation picard_MarkDuplicates picard_MarkDuplicatesWithMateCigar picard_MeanQualityByCycle picard_MergeBamAlignment picard_MergeSamFiles picard_NormalizeFasta picard_QualityScoreDistribution picard_ReorderSam picard_ReplaceSamHeader picard_RevertOriginalBaseQualitiesAndAddMateCigar picard_RevertSam picard_SamToFastq picard_SortSam picard_ValidateSamFile Picard SAM/BAM manipulation tools. Sequencing Formatting 2889519
picard
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3.3.20220408 phyml PhyML is a phylogeny software based on the maximum-likelihood principle. Phylogenetics Bioinformatics Phylogenetics Phylogenetic tree generation (maximum likelihood and Bayesian methods) 8945
phyml
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1.50.0 phyloseq_add_rank_names phyloseq_from_biom phyloseq_from_dada2 phyloseq_plot_bar phyloseq_plot_ordination phyloseq_plot_richness phyloseq_tax_glom Handling and analysis of high-throughput microbiome census data Microbiology Sequence analysis Metagenomics Deposition Analysis Visualisation 6744
bioconductor-phyloseq
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1.3.2 pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes Metagenomics Sequence sites, features and motifs Workflows Functional, regulatory and non-coding RNA Genome annotation Antimicrobial resistance prediction tRNA gene prediction Formatting Sequence assembly 34074
pharokka
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1.2.0 pgx_freqplot pgx_loader pgxLoader and pgxFreqplot functions from pgxRpi 0
bioconductor-pgxrpi
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0.9.6 iuc_pear PEAR evaluates all possible paired-end read overlaps Sequence assembly Sequence merging 74665
pear
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1.0 peakzilla Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. 120
python
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1.0.2 pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. 51627
openjdk
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3.5.0 bam2fastx Convert PacBio Bam File to fasta or fastq file 1209
pbtk
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1.17.0 pbmm2 A minimap2 SMRT wrapper for PacBio data. Mapping Pairwise sequence alignment Sorting 366
pbmm2
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2.0.2 pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference Mapping Variant calling 0
pbgcpp
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1.34.0 pathview Pathview is a tool set for pathway based data integration and visualization. Molecular interactions, pathways and networks Systems biology Data visualisation Pathway or network analysis Pathway or network visualisation 50297
bioconductor-pathview
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1.0.2 parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. 3171
parse_mito_blast
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4.3 pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. Virology Tree-based sequence alignment Variant classification 59046
pangolin
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1.5.2 panaroo A Bacterial Pangenome Analysis Pipeline Workflows Sequence assembly Gene and protein families Plant biology Sequencing De-novo assembly Genome assembly Clustering 387
panaroo
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1.1.3 pairtools_dedup pairtools_parse pairtools_sort pairtools_split pairtools_stats Flexible tools for Hi-C data processing 1218
pairtools
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0.0.5 pacu_map pacu_snp PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. Phylogenetics Sequence analysis Clustering 165
pacu_snp
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0.1 packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection 0
python
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2.5.5 orthofinder_onlygroups Accurate inference of orthologous gene groups made easy Phylogenetics Phylogenomics Bioinformatics Comparative genomics Sequence analysis Genome comparison Phylogenetic tree generation (from molecular sequences) Phylogenetic tree analysis Genome alignment 11277
orthofinder
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0.0.4 orfipy Galaxy wrapper for ORFIPY Computer science RNA-Seq Transcriptomics Small molecules Coding region prediction Database search Transcriptome assembly De-novo assembly 9855
orfipy
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1.3.5 optitype Precision HLA typing from NGS data 1881
optitype
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v2.0.2 optdoe Optimal Design Of Experiment 0
doebase
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1.45 onto_tk_get_ancestor_terms onto_tk_get_child_terms onto_tk_get_descendent_terms onto_tk_get_parent_terms onto_tk_get_parent_terms_by_relationship_type onto_tk_get_relationship_id_vs_relationship_def onto_tk_get_relationship_id_vs_relationship_name onto_tk_get_relationship_id_vs_relationship_namespace onto_tk_get_relationship_types onto_tk_get_root_terms onto_tk_get_subontology_from onto_tk_term_id_vs_term_def onto_tk_term_id_vs_term_name onto_tk_get_term_synonyms onto_tk_get_terms onto_tk_get_terms_by_relationship_type onto_tk_obo2owl onto_tk_obo2rdf onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. 1551
perl-onto-perl
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3.1.3 ont_fast5_api_compress_fast5 ont_fast5_api_fast5_subset ont_fast5_api_multi_to_single_fast5 ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. 9270
ont-fast5-api
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0.3.1 omark Proteome quality assessment software Proteomics Sequence analysis Statistics and probability Sequence assembly validation Differential protein expression profiling 2223
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0.3 odgi_build odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. 87
odgi
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0.1.2.6 ococo Variant detection of SNVs 10164
ococo
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1.2.13 obi_illumina_pairend obi_ngsfilter obi_annotate obi_clean obi_convert obi_grep obi_sort obi_stat obi_tab obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files Sequence analysis DNA Sequencing Sequence analysis Sequence analysis 139449
obitools
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2.3.3 nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. Sequencing Genomics Duplication detection Sequence analysis 0
nudup
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4.3.1 novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. 36009
novoplasty
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3.5.5 nonpareil Estimate average coverage in metagenomic datasets Operation 813
nonpareil
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ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. Genomics Transcriptomics Read pre-processing Sequencing quality control Variant calling Formatting Sequence contamination filtering 169773
ngsutils
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0.2.7 ngmlr CoNvex Gap-cost alignMents for Long Reads Sequencing Mapping DNA structural variation DNA mapping Sequence alignment Genetic variation analysis 4218
ngmlr
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2.7.0 nextalign nextclade Identify differences between your sequences and a reference sequence used by Nextstrain Genomics Sequence analysis Cladistics Methylation analysis Variant calling 55863
nextalign
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1.6+galaxy1 newick_display Perform operations on Newick trees Phylogeny Genomics Computer science Phylogenetic tree generation Phylogenetic tree analysis Phylogenetic tree reconstruction 192177
newick_utils
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0.0.1_update20200803 necat Error correction and de-novo assembly for ONT Nanopore reads Sequence assembly De-novo assembly 2925
necat
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0.5.5 ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). Sequence analysis Sequence assembly Sequence assembly validation Sequence trimming Sequence contamination filtering 20310
ncbi-fcs-gx
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1.70 ncbi_eutils_ecitmatch ncbi_eutils_efetch ncbi_eutils_einfo ncbi_eutils_elink ncbi_eutils_epost ncbi_eutils_esearch ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases 8561
python
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22.4 ncbi_entrez_direct_efetch ncbi_entrez_direct_einfo ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases 3
entrez-direct
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17.1.0 datasets_download_gene datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. Biological databases Data handling Sequence database search Data retrieval 62412
ncbi-datasets-cli
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0.2.8 ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API 104394
ncbi-acc-download
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0.6.11 nanopolishcomp_eventaligncollapse nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. Sequence analysis Sequencing Genetic variation Methylation analysis Collapsing methods 3360
nanopolishcomp
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1.44.1 nanoplot Plotting tool for long read sequencing data and alignments Genomics Scatter plot plotting Box-Whisker plot plotting 576358
nanoplot
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1.0.0rc3.post2 nanocompore_db nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Functional, regulatory and non-coding RNA RNA-Seq Gene transcripts Transcriptomics Transcription factors and regulatory sites Post-translation modification site prediction PolyA signal detection Genotyping k-mer counting 3450
nanocompore
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0.1.2 bicodon_counts_from_fasta codon_freq_from_bicodons find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) 684
naltorfs
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3.9.0 mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data Proteomics Metabolomics Proteomics experiment Small molecules Natural product identification Standardisation and normalisation Peptide database search Deisotoping Clustering Filtering Chromatographic alignment Peak detection Peptide identification Chromatogram visualisation Mass spectrum visualisation Structure visualisation Plotting Heat map generation 33
mzmine
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0.10.0 mykrobe_predict Antibiotic resistance predictions Whole genome sequencing Genotype and phenotype Probes and primers Genetic variation Metagenomics Antimicrobial resistance prediction Variant calling Genotyping Sequence trimming 0
mykrobe
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0.1.6 cluster_analyze_embed_muon mudata_import_export plot_muon preprocess_muon muon is a Python framework for multimodal omics analysis Cell biology Single-cell sequencing Gene expression Epigenetics Multiomics 0
muon
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4.0.0 mummer_delta_filter mummer_dnadiff mummer_mummer mummer_mummerplot mummer_nucmer mummer_show_coords Mummer4 Tools Sequence analysis Human genetics Multiple sequence alignment 193353
mummer4
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1.27 multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report Sequencing Bioinformatics Sequence analysis Genomics Validation Sequencing quality control 1411425
multiqc
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1.12.0 multigsea GSEA-based pathway enrichment analysis for multi-omics data Metabolomics Molecular interactions, pathways and networks Proteomics Transcriptomics Small molecules Gene-set enrichment analysis Aggregation Pathway analysis 477
bioconductor-multigsea
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0.74.0 multigps Analyzes collections of multi-condition ChIP-seq data. 1720
fonts-conda-ecosystem
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0.1.2 msaboot A multiple sequences alignment bootstrapping tool. 6317
msaboot
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1.0 mothur_align_check mothur_align_seqs mothur_amova mothur_anosim mothur_bin_seqs mothur_biom_info mothur_chimera_bellerophon mothur_chimera_ccode mothur_chimera_check mothur_chimera_perseus mothur_chimera_pintail mothur_chimera_slayer mothur_chimera_uchime mothur_chimera_vsearch mothur_chop_seqs mothur_classify_otu mothur_classify_seqs mothur_classify_tree mothur_clearcut mothur_cluster_classic mothur_cluster_fragments mothur_cluster_split mothur_cluster mothur_collect_shared mothur_collect_single mothur_consensus_seqs mothur_cooccurrence mothur_corr_axes mothur_count_groups mothur_count_seqs mothur_create_database mothur_degap_seqs mothur_deunique_seqs mothur_deunique_tree mothur_dist_seqs mothur_dist_shared mothur_fastq_info mothur_filter_seqs mothur_filter_shared mothur_get_communitytype mothur_get_coremicrobiome mothur_get_dists mothur_get_group mothur_get_groups mothur_get_label mothur_get_lineage mothur_get_mimarkspackage mothur_get_otulabels mothur_get_otulist mothur_get_oturep mothur_get_otus mothur_get_rabund mothur_get_relabund mothur_get_sabund mothur_get_seqs mothur_get_sharedseqs mothur_heatmap_bin mothur_heatmap_sim mothur_homova mothur_indicator mothur_lefse mothur_libshuff mothur_list_otulabels mothur_list_seqs mothur_make_biom mothur_make_contigs mothur_make_design mothur_make_fastq mothur_make_group mothur_make_lefse mothur_make_lookup mothur_make_shared mothur_make_sra mothur_mantel mothur_merge_count mothur_merge_files mothur_merge_groups mothur_merge_sfffiles mothur_merge_taxsummary mothur_metastats mothur_mimarks_attributes mothur_nmds mothur_normalize_shared mothur_otu_association mothur_otu_hierarchy mothur_pairwise_seqs mothur_parse_list mothur_parsimony mothur_pca mothur_pcoa mothur_pcr_seqs mothur_phylo_diversity mothur_phylotype mothur_pre_cluster mothur_primer_design mothur_rarefaction_shared mothur_rarefaction_single mothur_remove_dists mothur_remove_groups mothur_remove_lineage mothur_remove_otulabels mothur_remove_otus mothur_remove_rare mothur_remove_seqs mothur_rename_seqs mothur_reverse_seqs mothur_screen_seqs mothur_sens_spec mothur_seq_error mothur_sffinfo mothur_shhh_flows mothur_shhh_seqs mothur_sort_seqs mothur_split_abund mothur_split_groups mothur_sub_sample mothur_summary_qual mothur_summary_seqs mothur_summary_shared mothur_summary_single mothur_summary_tax mothur_taxonomy_to_krona mothur_tree_shared mothur_trim_flows mothur_trim_seqs mothur_unifrac_unweighted mothur_unifrac_weighted mothur_unique_seqs mothur_venn Mothur wrappers Microbial ecology Taxonomy Sequence analysis Phylogeny DNA barcoding Sequencing quality control Sequence clustering Taxonomic classification Visualisation Sequence read processing Phylogenetic analysis 3253677
mothur
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0.3.10 mosdepth fast and flexible BAM/CRAM depth calculation 65037
mosdepth
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1.3.4.6 moabs MOABS for differential methylation analysis on Bisulfite sequencing data. 945
moabs
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1.16.0 mmuphin MMUPHin is an R package implementing meta-analysis methods for microbial community profiles 0
bioconductor-mmuphin
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17-b804f mmseqs2_easy_linclust_clustering mmseqs2_taxonomy_assignment MMseqs2 is an ultra fast and sensitive sequence search and clustering suite Metagenomics Sequence analysis Proteins Nucleic acids Gene and protein families Taxonomy Sequence similarity search Sequence alignment Sequence clustering Taxonomic classification 0
mmseqs2
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2.22.0 mlst mlst_list Scan contig files against PubMLST typing schemes Immunoproteins and antigens Multilocus sequence typing 121091
mlst
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1.1.7 mitos mitos2 de-novo annotation of metazoan mitochondrial genomes Zoology Whole genome sequencing Genome annotation 968571
mitos
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1.9.1 mitobim assemble mitochondrial genomes 5061
mitobim
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1.1 mirnature Computational detection of canonical microRNAs 66
mirnature
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0.2.13 mirmachine Tool to detect miRNA in genome sequences 21
mirmachine
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0.13 miniprot miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. Sequence sites, features and motifs Sequence analysis Sequence alignment Protein sequence analysis 16086
miniprot
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2.28 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences Mapping Pairwise sequence alignment 1649653
minimap2
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0.3_r179 miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) Genomics Sequence assembly De-novo assembly 70144
miniasm
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3.2.6 minia Short-read assembler based on a de Bruijn graph Sequence assembly Genome assembly 22380
minia
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1.0.3 migmap mapper for full-length T- and B-cell repertoire sequencing Immunoproteins, genes and antigens Sequence analysis Sequence analysis Read mapping 6918
migmap
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1.3.3 microsatbed Select microsatellites for a bed file 4851
python
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0.10.4 mg_toolkit_bulk_download mg_toolkit_original_metadata Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. Metagenomics Data retrieval 39
mg-toolkit
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1.3.0 metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis Whole genome sequencing Metagenomic sequencing Metagenomics Read binning Sequence assembly Genome annotation Sequence trimming Demultiplexing 2766
metawrap-mg
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4.1.1 customize_metaphlan_database extract_metaphlan_database merge_metaphlan_tables metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis Metagenomics Phylogenomics Taxonomic classification Taxonomic classification 111196
metaphlan
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1.16.0-0.0.1 metagenomeseq_normalizaton metagenomeSeq Normalization Metagenomics Sequencing Sequence visualisation Statistical calculation 2960
bioconductor-metagenomeseq
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7.bba0d80 metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. Metagenomics Gene and protein families Homology-based gene prediction 1488
metaeuk
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1.0.5 metabuli_classify Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences Taxonomy Taxonomic classification 0
metabuli
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2.17 metabat2_jgi_summarize_bam_contig_depths metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. Metagenomics Sequence assembly Metagenomic sequencing Read binning Sequence assembly Genome annotation 36762
metabat2
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1.3 meryl_arithmetic_kmers meryl_count_kmers meryl_filter_kmers meryl_groups_kmers meryl_histogram_kmers meryl_print meryl_trio_mode Meryl a k-mer counter. Whole genome sequencing Genomics Sequence analysis Sequencing k-mer counting 633
merqury
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1.1.1 merquryfk_asmplot merquryfk_cnplot merquryfk_hapmaker merquryfk_happlot merquryfk_merquryfk FastK based version of Merqury 0
merquryfk
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1.3 merqury merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. Sequence assembly Whole genome sequencing Plant biology Genome assembly k-mer counting Scaffolding Phasing De-novo assembly 19680
merqury
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1.1.2 merlin Pedigree Analysis package GWAS study Mapping Haplotype mapping Genetic mapping 0
merlin
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0.8.5 meningotype Assign sequence type to N. meningitidis genome assemblies Microbiology Genotype and phenotype Genotyping Multilocus sequence typing 0
meningotype
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4.11.2 meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. 43529
graphicsmagick
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5.5.6 meme_dreme meme_fimo meme_meme meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. Data mining Sequence analysis Genetic variation Statistics and probability Nucleic acid feature detection Protein feature detection Statistical calculation 114435
meme
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6.21.7 megan_blast2lca megan_blast2rma megan_daa2info megan_daa2rma megan_daa_meganizer megan_read_extractor megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). Sequence analysis Sequence analysis Taxonomic classification 13857
megan
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1.1.3 megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) Metagenomics Sequencing Ecology Sequence assembly Genome assembly 2675
megahit
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1.2.9 megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Metagenomics Sequencing Ecology Sequence assembly Genome assembly 129168
megahit
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1.7.2 medaka_consensus medaka_consensus_pipeline medaka_snp medaka_variant Sequence correction provided by ONT Research Sequence assembly Machine learning Base-calling Variant calling Sequence assembly 597720
medaka
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mcl
22.282 mcl The Markov Cluster Algorithm, a cluster algorithm for graphs Molecular interactions, pathways and networks Clustering Network analysis Gene regulatory network analysis 459
mcl
mcl
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maxbin2 clusters metagenomic contigs into bins Metagenomics Sequence assembly Microbiology Sequence assembly 22903
maxbin2
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1.49.3 masigpro Identify significantly differential expression profiles in time-course microarray experiments Gene expression Molecular genetics Microarray experiment RNA-Seq Regression analysis 3142
coreutils
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3.1.3 mashmap Fast local alignment boundaries 6873
mashmap
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2.3 mash_screen mash_sketch Fast genome and metagenome distance estimation using MinHash Genomics Metagenomics Statistics and probability Sequence analysis DNA mutation Sequence distance matrix generation 37515
mash
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2.1.1b mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. Functional, regulatory and non-coding RNA Sequence analysis Sequence sites, features and motifs k-mer counting 27687
perl
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0.2.0 map_param_value Map a parameter value to another value 21126
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0.5.3 malt_run Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. 75
malt
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2.31.11 maker maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genomics DNA Sequence analysis Genome annotation 63496
maker
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0.5.9.2 mageck_count mageck_gsea mageck_mle mageck_pathway mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Genetics Genetic variation Genomics Genetic variation analysis 84607
mageck
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1.0.2+galaxy0 maf_stats1 MAF Coverage statistics 2921
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2.2.9.1 macs2_bdgbroadcall macs2_bdgcmp macs2_bdgdiff macs2_bdgpeakcall macs2_callpeak macs2_filterdup macs2_predictd macs2_randsample macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq ChIP-seq Molecular interactions, pathways and networks Transcription factors and regulatory sites Peak calling Enrichment analysis Gene regulatory network analysis 899197
macs2
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1.18.0 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. Metagenomics Statistics and probability Filtering Statistical calculation Standardisation and normalisation Visualisation 9327
bioconductor-maaslin2
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2.1.0 m6anet m6anet to detect m6A RNA modifications from nanopore data RNA-Seq Transcriptomics RNA Machine learning Quantification Imputation Gene expression profiling 132
m6anet
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0.3.1 lumpy_prep lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery 6363
lumpy-sv
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20 lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Genotype and phenotype Sequence analysis Genotyping 2709
lorikeet
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2.1.5 lofreq_alnqual lofreq_call lofreq_filter lofreq_indelqual lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. 14566693
lofreq
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2.0.1 links Scaffold genome assemblies with long reads. Sequence assembly Mapping Sequencing Scaffolding Genome assembly Read mapping Read pre-processing Sequence trimming 3675
links
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1.6.0 lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) Metagenomics Gene transcripts Evolutionary biology Sequencing Genetic variation Variant calling 117
r-base
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3.58.1 limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline Molecular biology Genetics RNA-Seq analysis 260233
bioconductor-limma
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0.1.2 length_and_gc_content Gets gene length and gc content from a fasta and a GTF file 22091
r-optparse
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0.5.1 legsta Performs in silico Legionella pneumophila sequence based typing. Public health and epidemiology Sequence analysis 309
legsta
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1.0.2 lcrgenie Ligase Chain Reaction Genie 0
lcr_genie
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1.04.22 lastz_wrapper_2 lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d Genomics Sequence alignment Read mapping 868122
lastz
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1205 last_al last_db last_split last_train last_maf_convert LAST finds similar regions between sequences. Genomics Comparative genomics Sequence alignment 1149
last
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1.0.1 krocus Predict MLST directly from uncorrected long reads Public health and epidemiology Multilocus sequence typing k-mer counting 0
krocus
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1.2 krakentools_alpha_diversity krakentools_beta_diversity krakentools_combine_kreports krakentools_extract_kraken_reads krakentools_kreport2krona krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken Taxonomy Metagenomics Visualisation Aggregation 419685
krakentools
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0.0.3 kraken_taxonomy_report Kraken taxonomy report Metagenomics Taxonomy Visualisation Classification 29594
biopython
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1.2.0 kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Metagenomics Taxonomy Genome annotation Taxonomic classification 13311
kraken-biom
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1.3.0 kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model Genomics Structure analysis Sequence analysis Gene functional annotation 4938
kofamscan
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1.0.1 kmer2stats A tool for creating data files for statistics based on kmers 0
kmer2stats
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kma
1.4.14 kma_map Map with KMA 3
kma
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2.3.2 kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) Public health and epidemiology Metagenomics Population genomics Sequence assembly Whole genome sequencing Multilocus sequence typing Genome assembly Virulence prediction 1950
kleborate
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2.2.7 king Kinship-based INference for Gwas 24
king
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3.0.0a3 khmer_abundance_distribution_single khmer_abundance_distribution khmer_count_median khmer_partition khmer_extract_partitions khmer_filter_abundance khmer_filter_below_abundance_cutoff khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more Sequence assembly Standardisation and normalisation De-novo assembly 15755
khmer
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1.0.2 kc-align Kc-Align custom tool Mapping Multiple sequence alignment 26064
kcalign
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0.48.0 kallisto_pseudo kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. Transcriptomics RNA-Seq Gene expression Gene expression profiling 344792
kallisto
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1.10.1 kaiju_addtaxonnames kaiju_mergeoutputs kaiju_kaiju kaiju_kaiju2krona kaiju_kaiju2table taxonomic classification of high-throughput sequencing reads Metagenomics Taxonomic classification 0
kaiju
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20201223 jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics 65778
jvarkit-wgscoverageplotter
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jq
1.0 jq JQ is a lightweight and flexible command-line JSON processor 5621
jq
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1.0 join_files_by_id This tool will join datasets according to a column with identifier 0
r-data.table
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jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Sequence analysis Genomics k-mer counting 14067
kmer-jellyfish
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0.8.4 jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) 22039
jcvi
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1.16.11 jbrowse_to_standalone jbrowse JBrowse Genome Browser integrated as a Galaxy Tool Genomics Genome visualisation 184589
jbrowse
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1.0.11 jasminesv Merge structural variants across samples 282
jasminesv
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1.0.0 iwtomics_loadandplot iwtomics_plotwithscale iwtomics_testandplot Interval-Wise Testing for Omics Data Statistics and probability Differential gene expression analysis Differentially-methylated region identification Peak calling Genome annotation Comparison 3806
bioconductor-iwtomics
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1.4.4 ivar_consensus ivar_filtervariants ivar_removereads ivar_trim ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Virology Primer removal 4525941
ivar
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1.20.0 isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. Computational biology Gene transcripts Sequence comparison Sequence analysis 12969
bioconductor-isoformswitchanalyzer
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1.7.2.3 isescan "ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements." Genomics DNA structural variation Sequence analysis Genetic variation Structural variation detection 209232
isescan
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1.2.0 irma Iterative Refinement Meta-Assembler (IRMA) is a tool to construct assembly of highly variable RNA viruses. Mapping assembly 22644
irma
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1.0.5 irissv Refine insertion sequences 87
samtools
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2.4.0 iqtree Efficient phylogenomic software by maximum likelihood Phylogenetics Phylogenetic analysis Sequence analysis 234711
iqtree
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0.1.0+galaxy0 ipfp_norm Normalisation algorithm used to adjust matrices iteratively to satisfy specific row and column sum constraints while preserving the data structure. 0
numpy
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0.6.5 intervene_pairwise intervene_upset Create pairwise and upset plots Computational biology Sequence comparison Sequence visualisation 19084
intervene
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1.0.1+galaxy1 Interval2Maf1 Extract MAF blocks given a set of intervals Sequence analysis 21392
bx-python
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5.59-91.0 interproscan Interproscan queries the interpro database and provides annotations. Gene and protein families Sequence analysis Sequence motif recognition Protein feature detection 205836
interproscan
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0.0.1 galaxy_intermine_exchange InterMine Exporter 667
coreutils
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2.0.5 integron_finder "IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching" Functional genomics Mobile genetic elements Molecular biology Sequence analysis Nucleic acid feature detection Sequence motif recognition Protein feature detection Genome annotation 217041
integron_finder
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1.5.3 instrain_compare instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes Mapping Metagenomics SNP detection Genome comparison 318
instrain
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1.22.0 infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data Heat map generation Expression analysis RNA-Seq analysis Copy number variation detection Clustering 87
bioconductor-infercnv
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2.15.2 iedb_api Get epitope binding predictions from IEDB-API 4770
python
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0.45 idr_download_by_ids Image Data Resource downloading tool 1917
omero-py
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idr
2.0.3 idr Galaxy wrappers for the IDR package from Nathan Boleu 14561
idr
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idba_hybrid idba_tran idba_ud Wrappers for the idba assembler variants. Sequence assembly Sequence assembly 8328
idba
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1.3.3 icescreen identification of ICEs and IMEs in Bacillota genomes. Mobile genetic elements Sequence sites, features and motifs Genomics Molecular interactions, pathways and networks Structural variation Database search Protein feature detection 0
icescreen
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1.0.3 hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies Sequence assembly Genomics Optimisation and refinement Genome assembly 1515
hypo
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2.5.47 hyphy_absrel hyphy_annotate hyphy_bgm hyphy_busted hyphy_cfel hyphy_conv hyphy_fade hyphy_fel hyphy_fubar hyphy_gard hyphy_meme hyphy_prime hyphy_relax hyphy_slac hyphy_sm19 hyphy_strike_ambigs hyphy_summary Hypothesis Testing using Phylogenies Phylogeny Small molecules Molecular interactions, pathways and networks Statistical calculation 62627
hyphy
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2.1.6 hybpiper Analyse targeted sequence capture data Phylogenetics Plant biology Gene transcripts Sequence assembly Phylogenomics Sequence trimming Sequence assembly Read mapping 5334
hybpiper
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3.9 humann humann_barplot humann_join_tables humann_reduce_table humann_regroup_table humann_rename_table humann_renorm_table humann_split_stratified_table humann_split_table humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution Metagenomics Phylogenomics Species frequency estimation Taxonomic classification Phylogenetic analysis 109527
humann
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2.0.5 htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) Sequence analysis Nucleic acid sequence analysis 1385415
htseq
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4.11 homer_annotatePeaks homer_findMotifs homer_findMotifsGenome homer_gtf_to_annotations homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. Sequence motif discovery 30569
homer
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3.4 hmmer_alimask hmmer_hmmalign hmmer_hmmbuild hmmer_hmmconvert hmmer_hmmemit hmmer_hmmfetch hmmer_hmmscan hmmer_hmmsearch hmmer_jackhmmer hmmer_nhmmer hmmer_nhmmscan hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). Sequence analysis Sequence sites, features and motifs Gene and protein families Formatting Multiple sequence alignment Sequence profile generation Format validation Conversion Sequence generation Data retrieval Statistical calculation Database search Formatting Database search Database search Probabilistic sequence generation Statistical calculation Statistical calculation Sequence database search Formatting Sequence database search Database search Sequence database search 126061
hmmer
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1.3.1 hivclustering Infers transmission networks from pairwise distances inferred by tn93 0
python-hivclustering
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2.2.1 hisat2 HISAT2 is a fast and sensitive spliced alignment program. RNA-seq Sequence alignment 3945447
hisat2
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0.3.1 hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. Sequence assembly Metagenomics Sequence assembly 1371
hifiasm_meta
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0.25.0 hifiasm A fast haplotype-resolved de novo assembler 20091
hifiasm
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3.2.4 hicstuff_pipeline A toolkit to generate and manipulate Hi-C matrices 0
hicstuff
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3.7.6 hicexplorer_chicaggregatestatistic hicexplorer_chicdifferentialtest hicexplorer_chicexportdata hicexplorer_chicplotviewpoint hicexplorer_chicqualitycontrol hicexplorer_chicsignificantinteractions hicexplorer_chicviewpoint hicexplorer_chicviewpointbackgroundmodel hicexplorer_hicadjustmatrix hicexplorer_hicaggregatecontacts hicexplorer_hicaverageregions hicexplorer_hicbuildmatrix hicexplorer_hicbuildmatrixmicroc hicexplorer_hiccomparematrices hicexplorer_hiccompartmentspolarization hicexplorer_hicconvertformat hicexplorer_hiccorrectmatrix hicexplorer_hiccorrelate hicexplorer_hicdetectloops hicexplorer_hicdifferentialtad hicexplorer_hicfindrestrictionsites hicexplorer_hicfindtads hicexplorer_hichyperoptDetectLoops hicexplorer_hicinfo hicexplorer_hicinterintratad hicexplorer_hicmergedomains hicexplorer_hicmergeloops hicexplorer_hicmergematrixbins hicexplorer_hicnormalize hicexplorer_hicpca hicexplorer_hicplotaverageregions hicexplorer_hicplotdistvscounts hicexplorer_hicplotmatrix hicexplorer_hicplotsvl hicexplorer_hicplotviewpoint hicexplorer_hicquickqc hicexplorer_hicsummatrices hicexplorer_hictransform hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. 174423
hicexplorer
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0.1.0 hgvsparser Parsing and building variant descriptor strings compliant with the HGVS standard 19059
r-base
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1.0 heinz_bum heinz heinz_scoring heinz_visualization An algorithm for identification of the optimal scoring subnetwork. Genetics Gene expression Molecular interactions, pathways and networks Pathway or network analysis 11015
bioconductor-bionet
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3.2.0 ggplot2_heatmap2 heatmap.2 function from the R gplots package 400029
r-gplots
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0.3.14 som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. Genomics DNA polymorphism Variant calling Sequence analysis Genotyping 0
hap.py
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1.3.8 hapog Hapo-G - Haplotype-Aware Polishing of Genomes Sequence assembly Genomics Genome assembly Optimisation and refinement 3009
hapog
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1.3.4 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies Haplotype mapping Variant classification 369
hapcut2
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2.6.1 bio_hansel Heidelberg and Enteritidis SNP Elucidation Whole genome sequencing DNA polymorphism Genotype and phenotype Infectious disease Agricultural science Genotyping SNP detection Genome assembly 2155
bio_hansel
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1.1.4 hamronize_summarize hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. Public health and epidemiology Microbiology Bioinformatics Data handling Antimicrobial resistance prediction Parsing 28473
hamronization
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0.1.0 halfdeep HalfDeep: Automated detection of intervals covered at half depth by sequenced reads. 144
halfdeep
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0.1.0 gwastools_manhattan_plot GWAS study Deposition Analysis Annotation 63
bioconductor-gwastools
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0.1 gvcftools_extract_variants gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf. 0
gvcftools
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3.2.1 gubbins Gubbins - bacterial recombination detection Phylogeny Genotype and phenotype Whole genome sequencing Genotyping Phylogenetic inference Ancestral reconstruction 28849
gubbins
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357 gtftobed12 Convert GTF files to BED12 format Sequence analysis 62574
ucsc-gtftogenepred
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2.4.1 gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. Metagenomics Taxonomy Phylogenetics Database management Proteins Genome alignment Taxonomic classification Sequence assembly Query and retrieval 7254
gtdbtk
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0.1.9 gtdb_to_taxdump Convert GTDB taxonomy to NCBI taxdump format Computational biology Data handling Mapping Generation 1347
gtdb_to_taxdump
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1.1.2 groot GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples Metagenomics Microbiology Genomics Antimicrobial resistance prediction 96
groot
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graphlan graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees Metagenomics Phylogenetics Phylogenomics Cladistics Phylogenetic inference Phylogenetic tree visualisation Phylogenetic tree editing Taxonomic classification 42277
graphlan
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2.4 graphembed Compute a 2D embedding of a data matrix given supervised class information 606
graph_embed
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@TOOL_VERSION@+galaxy11 gprofiler_convert gprofiler_gost gprofiler_orth gprofiler_random gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more 37120
r-gprofiler2
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1.50.0 goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data RNA-Seq Gene functional annotation 165269
bioconductor-goseq
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2.0.1 goenrichment goslimmer Performs GO Enrichment analysis. Transcriptomics Gene-set enrichment analysis 48417
goenrichment
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3.02 glimmer_acgt_content glimmer_build_icm glimmer_extract glimmer_gbk_to_orf glimmer_glimmer_to_gff glimmer_long_orfs glimmer_knowledge_based glimmer_not_knowledge_based Glimmer makes gene predictions. Sequence analysis Sequence analysis Genetic variation analysis 13629
glimmer
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1.0 emc-ggupset Create Upset Plots with ggupset 0
r-ggupset
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3.4.0 ggplot2_heatmap ggplot2_pca ggplot2_histogram ggplot2_point ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. Data visualisation Visualisation 203604
r-base
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0.12.7 gffread gffread filters and/or converts GFF3/GTF2 records Nucleic acids Sequence analysis Sequence annotation 118278
gffread
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0.12.6 gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. Nucleic acids Sequence analysis Sequence annotation 35587
gffcompare
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1.2 gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) 4554
bcbiogff
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0.1.2 gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format 54434
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1.7.7.1 get_annotated_regions_from_gb get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. Cell biology Sequence assembly Whole genome sequencing Plant biology Model organisms De-novo assembly Genome assembly Mapping assembly Mapping Sequence trimming 11469
getorganelle
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0.5.9.2 get_hrun Annotate indel variants with homopolymer context 27
pyfaidx
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1.0.1 geopandas_table2geojson GeoPandas is an open source project to make working with geospatial data easier. 0
geopandas
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0.5+galaxy2 genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). 20176
genrich
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1.2.0 genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases RNA-Seq Transcriptomics Microbial ecology Genotype and phenotype Microarray experiment Gene-set enrichment analysis Essential dynamics Deposition Principal component visualisation Dimensionality reduction 165
bioconductor-genomicsupersignature
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2.0.1 genomescope Analyze unassembled short reads 25620
genomescope2
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genetrack Contains a tool that separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand. 1400
numpy
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4.7.1+galaxy1 gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. 735
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3.0.0 genehunter_modscore Maximised LOD score pedigree analysis utility 0
ghm
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1.0.1+galaxy0 GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals 3337
To update
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0.20.1 gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_db_info gemini_@BINARY@ gemini_@BINARY@ gemini_inheritance gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation Sequence analysis Sequence analysis Genetic variation analysis 32503
gemini
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0.29.1 gem_check_memote gem_escher_visualization gem_extract_exchange gem_flux_distribution gem_flux_variability_analysis gem_knockout gem_phenotype_phase_plane Tools for analyzing genome-scale metabolic models (GEMs) using COBRApy and related libraries. 0
cobra
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1.2 gecko Ungapped genome comparison 5259
gecko
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1.0.0 data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format 0
python
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4.1.7.0 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK 41341
gatk4
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1.8.17 funannotate_annotate funannotate_clean funannotate_compare funannotate_predict funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. Genomics Genome annotation 60648
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1.0.2 fsd fsd_beforevsafter fsd_regions td Tool that plots a histogram of sizes of read families 1716
matplotlib
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1.5.2 freyja_aggregate_plot freyja_boot freyja_demix freyja_variants lineage abundances estimation Metagenomics RNA-Seq quantification 74538
freyja
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11.6 control_freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. DNA structural variation Oncology Human genetics Data mining Copy number estimation Variant calling Genome alignment 4584
gawk
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1.3.9 freebayes bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool Genomics Genetic variation Rare diseases Variant calling Statistical calculation 1142475
freebayes
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fraggenescan Tool for finding (fragmented) genes in short read Genetics Sequence analysis Gene prediction 7411
fraggenescan
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1.2.11 flash Fast Length Adjustment of SHort reads Sequencing Sequence assembly Read pre-processing Sequence merging Sequence assembly 116362
flash
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1.5 flair_collapse flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. 6027
flair
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0.2.1 filtlong Filtlong - Filtering long reads by quality Filtering Sequencing quality control 331020
filtlong
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1.8.0+galaxy1 fgsea Perform gene set testing using fgsea Genetics Gene-set enrichment analysis 91962
bioconductor-fgsea
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r193 fermi2 fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. 0
fermi2
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0.2.1 feelnc Galaxy wrapper for FEELnc RNA-seq Functional, regulatory and non-coding RNA Annotation Classification 8333
feelnc
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2.0.8 featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome RNA-Seq Read summarisation RNA-Seq quantification 4972225
subread
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2.1.10 fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL Phylogenetics Sequence analysis Phylogenetic tree generation (from molecular sequences) Phylogenetic tree generation (maximum likelihood and Bayesian methods) 326681
fasttree
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0.3.1+galaxy0 fastqe FASTQE Sequence analysis Sequencing Sequencing quality control 63024
fastqe
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0.74+galaxy1 fastqc Read QC reports using FastQC Sequencing Data quality management Sequence analysis Sequence composition calculation Sequencing quality control Statistical calculation 16575871
fastqc
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3.0.1 fastq_dl Download FASTQ files from ENA. 444
fastq-dl
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0.24.1 fastp Fast all-in-one preprocessing for FASTQ files Sequence analysis Probes and primers Sequencing quality control Sequence contamination filtering 5325613
fastp
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1.1.0 fastk_fastk fastk_histex fastk_logex FastK: A K-mer counter (for HQ assembly data sets) Genomics Sequence analysis k-mer counting Sequence analysis 504
fastk
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1.3 fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity Microbiology Genetic variation Genome alignment Sequence similarity search 80742
fastani
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2.0 fasta-stats Display summary statistics for a fasta file. 310008
numpy
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1.0.1 fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. 3206
openjdk
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0.1 fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) Metagenomics Microbiology Public health and epidemiology Antimicrobial resistance Antimicrobial resistance prediction 5669
fargene
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1.2.4 falco A high throughput sequence QC analysis tool Workflows Mapping Imaging Sequencing quality control Visualisation Read mapping 18594
falco
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0.5.8 fairy_cov fairy_sketch Fast approximate contig coverage for metagenomic binning Metagenomics Read binning Sequence assembly validation 39
fairy
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3.0.3+galaxy3 Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. 328429
bx-python
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0.20 export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn Taxonomy Metabolomics Biomarkers Conversion 21800
export2graphlan
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2.4.0 exonerate Exonerate is a generic tool for pairwise sequence comparison. Sequence analysis Sequence sites, features and motifs Molecular interactions, pathways and networks Pairwise sequence alignment Protein threading Genome alignment 11336
exonerate
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1.1.0 exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data Exome sequencing Gene transcripts Mapping Sequencing Genetic variation Rare diseases Sequence analysis Variant calling Genotyping Copy number estimation 10870
r-exomedepth
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2.1.0 evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. Gene expression Gene structure Gene prediction 27
evidencemodeler
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3.1.3 ete_treeviewer A toolkit for the analysis and visualization of trees. Phylogenetics Phylogenetic analysis Phylogenetic tree editing 0
ete
curl
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0.3.2 episcanpy_build_matrix episcanpy_cluster_embed episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python Epigenomics Cell biology DNA Enrichment analysis Imputation 5067
episcanpy
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113.4 ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions 10425
ensembl-vep
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enasearch_retrieve_analysis_report enasearch_retrieve_data enasearch_retrieve_run_report enasearch_retrieve_taxons enasearch_search_data A Python library for interacting with ENA's API 6157
enasearch
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0.8.0 ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). 5727
ena-upload-cli
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5.0.0 EMBOSS: antigenic1 EMBOSS: backtranseq2 EMBOSS: banana3 EMBOSS: biosed4 EMBOSS: btwisted5 EMBOSS: cai6 EMBOSS: cai_custom6 EMBOSS: chaos7 EMBOSS: charge8 EMBOSS: checktrans9 EMBOSS: chips10 EMBOSS: cirdna11 EMBOSS: codcmp12 EMBOSS: coderet13 EMBOSS: compseq14 EMBOSS: cpgplot15 EMBOSS: cpgreport16 EMBOSS: cusp17 EMBOSS: cutseq18 EMBOSS: dan19 EMBOSS: degapseq20 EMBOSS: descseq21 EMBOSS: diffseq22 EMBOSS: digest23 EMBOSS: dotmatcher24 EMBOSS: dotpath25 EMBOSS: dottup26 EMBOSS: dreg27 EMBOSS: einverted28 EMBOSS: epestfind29 EMBOSS: equicktandem31 EMBOSS: est2genome32 EMBOSS: etandem33 EMBOSS: extractfeat34 EMBOSS: extractseq35 EMBOSS: freak36 EMBOSS: fuzznuc37 EMBOSS: fuzzpro38 EMBOSS: fuzztran39 EMBOSS: garnier40 EMBOSS: geecee41 EMBOSS: getorf42 EMBOSS: helixturnhelix43 EMBOSS: hmoment44 EMBOSS: iep45 EMBOSS: infoseq46 EMBOSS: isochore47 EMBOSS: lindna48 EMBOSS: marscan49 EMBOSS: maskfeat50 EMBOSS: maskseq51 EMBOSS: matcher52 EMBOSS: megamerger53 EMBOSS: merger54 EMBOSS: msbar55 EMBOSS: needle56 EMBOSS: newcpgreport57 EMBOSS: newcpgseek58 EMBOSS: newseq59 EMBOSS: noreturn60 EMBOSS: notseq61 EMBOSS: nthseq62 EMBOSS: octanol63 EMBOSS: oddcomp64 EMBOSS: palindrome65 EMBOSS: pasteseq66 EMBOSS: patmatdb67 EMBOSS: pepcoil68 EMBOSS: pepinfo69 EMBOSS: pepnet70 EMBOSS: pepstats71 EMBOSS: pepwheel72 EMBOSS: pepwindow73 EMBOSS: pepwindowall74 EMBOSS: plotcon75 EMBOSS: plotorf76 EMBOSS: polydot77 EMBOSS: preg78 EMBOSS: prettyplot79 EMBOSS: prettyseq80 EMBOSS: primersearch81 EMBOSS: revseq82 EMBOSS: seqmatchall83 EMBOSS: seqret84 EMBOSS: showfeat85 EMBOSS: shuffleseq87 EMBOSS: sigcleave88 EMBOSS: sirna89 EMBOSS: sixpack90 EMBOSS: skipseq91 EMBOSS: splitter92 EMBOSS: supermatcher95 EMBOSS: syco96 EMBOSS: tcode97 EMBOSS: textsearch98 EMBOSS: tmap99 EMBOSS: tranalign100 EMBOSS: transeq101 EMBOSS: trimest102 EMBOSS: trimseq103 EMBOSS: twofeat104 EMBOSS: union105 EMBOSS: vectorstrip106 EMBOSS: water107 EMBOSS: wobble108 EMBOSS: wordcount109 EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools Molecular biology Sequence analysis Biology Sequence analysis Local alignment Sequence alignment analysis Global alignment Sequence alignment 1484241
emboss
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6.6.0 emboss_needle emboss_needleall Galaxy wrappers for EMBOSS6 tools Molecular biology Sequence analysis Biology Sequence analysis Local alignment Sequence alignment analysis Global alignment Sequence alignment 6
emboss
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1.20.0 egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing Systems biology Gene set testing 31512
bioconductor-egsea
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3.36.0 edger Perform RNA-Seq differential expression analysis using edgeR pipeline Genetics RNA-Seq ChIP-seq Differential gene expression analysis 244139
bioconductor-edger
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0.1.1 ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases 5288
six
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0.1.2 drug2cell Collection of utility functions for gene group activity evaluation in scanpy. 0
drug2cell
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1.10.0 dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data Gene expression RNA-seq Sequencing Transcriptomics Loading Community profiling 34039
bioconductor-dropletutils
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3.6.2 drep_compare drep_dereplicate dRep compares and dereplicates genome sets Metagenomics Genomics Sequence analysis Genome comparison 4716
drep
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1.5.0 dram_annotate dram_distill dram_merge_annotations dram_neighborhoods dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function Metagenomics Biological databases Molecular genetics Gene functional annotation 23121
dram
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1.0.2 dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. 0
dnaweaver_synbiocad
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3.1.0 dnabot DNA assembly using BASIC on OpenTrons 0
dnabot
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disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler Structure determination Protein sequence analysis 5452
disco
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0.2.4 dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. 0
dimet
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3.12.0 diffbind Diffbind provides functions for processing ChIP-Seq data. ChIP-seq Differential binding analysis 77990
bioconductor-diffbind
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2.1.11 bg_diamond bg_diamond_makedb bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. Sequence analysis Proteins Sequence alignment analysis 470590
diamond
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1.48.0 dexseq dexseq_count plotdexseq Inference of differential exon usage in RNA-Seq RNA-Seq Enrichment analysis Exonic splicing enhancer prediction 125066
bioconductor-dexseq
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2.11.40.8 deseq2 Differential gene expression analysis based on the negative binomial distribution RNA-Seq Differential gene expression analysis RNA-Seq analysis 1036405
bioconductor-deseq2
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0.9.1 delly_call delly_classify delly_cnv delly_filter delly_lr delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. DNA structural variation Sequencing Pathology Genomics Genetic variation Bioinformatics Population genomics Rare diseases Indel detection Structural variation detection Variant calling Genotyping Genetic variation analysis 5469
delly
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1.1.0 deg_annotate Annotate DESeq2/DEXSeq output tables RNA-Seq analysis Gene functional annotation 201754
bedtools
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1.5.0 deepvariant DeepVariant is a deep learning-based variant caller 24849
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1.2.5 deepsig Predictor of signal peptides in proteins based on deep learning 546
deepsig
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1.4 deepmicro Representation learning and classification framework Microbial ecology Machine learning Pathology Public health and epidemiology Allergy, clinical immunology and immunotherapeutics Essential dynamics Splitting Community profiling 1677
deepmicro
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1.0.4 deeparg_predict deeparg_short_reads A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes Microbiology Antimicrobial resistance prediction Antimicrobial resistance prediction 0
deeparg
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1.0.0 decontaminator Deep Learning method for novel virus detection in sequencing data Metagenomics Filtering 408
numpy
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1.22.0 decontam Removes decontamination features (ASVs/OTUs) using control samples Metagenomics Microbial ecology Sequencing Classification 3
bioconductor-decontam
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1.8 datamash_ops datamash_reverse datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. 2874583
datamash
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1.0.0 data_source_iris_tcga IRIS-TCGA Data source tool 0
python
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1.1.7 Fasta_to_Contig2Bin das_tool DAS Tool for genome resolved metagenomics Metagenomics Read binning 16581
das_tool
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1.34.0 dada2_assignTaxonomyAddspecies dada2_dada dada2_filterAndTrim dada2_learnErrors dada2_makeSequenceTable dada2_mergePairs dada2_plotComplexity dada2_plotQualityProfile dada2_primerCheck dada2_removeBimeraDenovo dada2_seqCounts DADA2 wrappers Sequencing Genetic variation Microbial ecology Metagenomics Variant calling DNA barcoding 1136620
bioconductor-dada2
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1.1.1 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. 535
matplotlib
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2.1.2 cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. DNA structural variation Sequencing Computer science Split read mapping Genotyping Structural variation detection 1272
cutesv
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5.0 cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). Genomics Probes and primers Sequencing Sequence trimming Primer removal Read pre-processing 2316706
cutadapt
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0.7.0 crossmap_bam crossmap_bed crossmap_bw crossmap_gff crossmap_region crossmap_vcf crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies 22961
crossmap
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0.3 crosscontamination_barcode_filter Barcode contamination discovery tool Filtering Sequence contamination filtering Sequencing quality control RNA-Seq analysis 1267
r-ggplot2
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1+galaxy0 crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. Sequence analysis Genomics Data visualisation Visualisation 6234
crispr_studio
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0.7.0 coverm_contig coverm_genome CoverM genome and contig wrappers Metagenomics Sequence analysis Local alignment 5751
coverm
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0.0.4 CoverageReport2 Generate Detailed Coverage Report from BAM file 0
perl-number-format
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1.0.1 cosg Marker gene identification for single-cell sequencing data using COSG. Bioinformatics Nucleic acid sequence analysis 0
cosg
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1.1.0 concoct concoct_coverage_table concoct_cut_up_fasta concoct_extract_fasta_bins concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. Metagenomics Sequence clustering Read binning 25110
concoct
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0.1.0 compress_file Compress files. 77763
gzip
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0.1.1 compose_text_param Compose a text parameter value using text, integer and float values 182667
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0.2.6 compleasm Compleasm: a faster and more accurate reimplementation of BUSCO Sequence assembly Genomics Transcriptomics Sequence analysis Sequence assembly validation Sequence analysis Scaffolding Transcriptome assembly 2985
compleasm
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1.0 column_remove_by_header Remove columns by header 51595
python
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0.0.1 column_order_header_sort Sort Column Order by heading 19380
python
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2.1 Add_a_column1 Compute an expression on every row 11407163
python
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0.0.2 collection_element_identifiers Extract element identifiers of a collection 65351
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0.0.3 collection_column_join Column Join on Collections 171015
coreutils
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24.7.14 commet discosnp_rad discosnp_pp kissplice lordec mapsembler2 takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome 4868
commet
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1.5.5 colabfold_alphafold colabfold_msa Protein prediction based on AlphaFold2 Protein folds and structural domains Protein folding, stability and design Structure prediction Sequence sites, features and motifs Metagenomics Database search Protein structure prediction Fold recognition 27531
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0.9.3 cooc_mutbamscan cooc_pubmut cooc_tabmut co-occurrence of mutations on amplicons Genetic variation 8337
cojac
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4.9 codeml Detects positive selection Phylogenetics Sequence analysis Probabilistic sequence generation Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetic tree analysis 187000
paml
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0.9.12 cnvkit_access cnvkit_antitarget cnvkit_autobin cnvkit_batch cnvkit_export_bed cnvkit_breaks cnvkit_call cnvkit_export_cdt cnvkit_coverage cnvkit_diagram cnvkit_fix cnvkit_genemetrics cnvkit_heatmap cnvkit_export_jtv cnvkit_export_nexus_basic cnvkit_export_nexus_ogt cnvkit_reference cnvkit_scatter cnvkit_export_seg cnvkit_segment cnvkit_segmetrics cnvkit_sex cnvkit_target cnvkit_theta cnvkit_export_vcf detecting copy number variants and alterations genome-wide from high-throughput sequencing DNA structural variation Variant calling 3390
cnvkit
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2.0.0 cnv_vcf2json cnv-vcf2json Converts structural variants VCF file to JSON. 39
cnv-vcf2json
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1.0.2 cnv_phenopacket cnv-phenopacket Converts TSV metadata file to JSON. 21
cnv-phenopacket
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1.1.1 clustering_from_distmat Distance matrix-based hierarchical clustering using SciPy 369
python
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2.1 clustalw ClustalW multiple sequence alignment program for DNA or proteins Phylogeny Sequence analysis Multiple sequence alignment 503134
clustalw
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1.0.10 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling Molecular genetics Variant calling 15243
clair3
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1.4.4 cite_seq_count Count CMO/HTO Transcriptomics Immunoproteins and antigens RNA-Seq quantification 522
cite-seq-count
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0.69.8 circos_aln_to_links circos_binlinks circos_bundlelinks circos circos_gc_skew circos_resample circos_wiggle_to_scatter circos_wiggle_to_stacked circos_tableviewer circos_interval_to_text circos_interval_to_tile Build Circos Plots in Galaxy Sequence visualisation 271555
circos
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2.3.8 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. RNA splicing Gene transcripts Literature and language 2418
circexplorer2
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1.5.a chromeister ultra-fast pairwise genome comparisons 39324
chromeister
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1.0.9.post1 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing 51
chopin2
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1.4.3 chira_collapse chira_extract chira_map chira_merge chira_quantify Chimeric Read Annotator for RNA-RNA interactome data RNA Molecular interactions, pathways and networks Functional, regulatory and non-coding RNA 128574
chira
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chewbbaca_allelecall chewbbaca_allelecallevaluator chewbbaca_createschema chewbbaca_downloadschema chewbbaca_extractcgmlst chewbbaca_joinprofiles chewbbaca_nsstats chewbbaca_prepexternalschema BSR-Based Allele Calling Algorithm 3906
chewbbaca
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0.7 cherri_eval cherri_train Computational Help Evaluating RNA-RNA interactions Molecular interactions, pathways and networks Structure analysis Machine learning 621
cherri
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1.0.2 checkm2 Rapid assessment of genome bin quality using machine learning Genomics Phylogenomics Phylogenetics Taxonomy Metagenomics Data quality management Sequence assembly validation Validation Sequence composition calculation Sequencing quality control Statistical calculation 0
checkm2
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1.2.3 checkm_analyze checkm_lineage_set checkm_lineage_wf checkm_plot checkm_qa checkm_taxon_set checkm_taxonomy_wf checkm_tetra checkm_tree checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes Genomics Phylogenomics Phylogenetics Taxonomy Metagenomics Data quality management Sequence assembly validation Validation Sequence composition calculation Sequencing quality control Statistical calculation 35892
checkm-genome
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1.0.1 charts Enables advanced visualization options in Galaxy Charts 42431
r-getopt
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1.30.0 cemitool Gene co-expression network analysis tool Gene expression Transcriptomics Microarray experiment Enrichment analysis Pathway or network analysis 2418
bioconductor-cemitool
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4.8.1 cd_hit Cluster or compare biological sequence datasets Sequencing Sequence clustering 41199
cd-hit
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5.2.3 cat_add_names cat_bins cat_contigs cat_prepare cat_summarise Contig Annotation Tool (CAT) Metagenomics Metagenomic sequencing Taxonomy Sequence assembly Taxonomic classification Sequence assembly Coding region prediction 56590
cat
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2.0.7 biobox_add_taxid cami_amber cami_amber_add cami_amber_convert Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments Metagenomics Read binning 25155
cami-amber
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0.1.0 calculate_numeric_param Calculate a numeric parameter value using integer and float values. 5172
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1.0.0 calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. 0
numpy
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2.7.1 cactus_cactus cactus_export Cactus is a reference-free whole-genome multiple alignment program Genomics Sequence analysis Phylogeny Sequence assembly Mapping Phylogenetics Multiple sequence alignment Genome alignment 8502
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0.2.7 bwameth Fast and accurate alignment of BS-seq reads 55497
bwameth
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2.2.1 bwa_mem2_idx bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. Mapping Sequence alignment 458067
bwa-mem2
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bwa
0.7.19 bwa_mem bwa Wrapper for bwa mem, aln, sampe, and samse Mapping Genome indexing Sequence alignment Read mapping Sequence alignment Generation Sequence alignment Generation Sequence alignment Sequence alignment 4956328
bwa
bwa
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5.8.0 busco BUSCO assess genome and annotation completeness Sequence assembly Genomics Transcriptomics Sequence analysis Sequence assembly validation Scaffolding Genome assembly Transcriptome assembly 623384
busco
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1.0.2 brew3r_r Extend 3' end of a GTF using another GTF as a template Transcriptomics Genomics Genome annotation 36
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0.35.5 breseq Predicts mutations in microbial genomes Sequencing Sequence analysis DNA mutation Polymorphism detection 12599
breseq
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3.1 est_abundance Bayesian Reestimation of Abundance with KrakEN Metagenomics Microbial ecology Statistical calculation 312987
bracken
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2.5.3 bowtie2 Bowtie2: Fast and sensitive read alignment Mapping Genomics Mapping Read mapping 3729303
bowtie2
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1.1 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 3338
bcbiogff
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1.7.0 magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome 20853
magicblast
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2.3.3 biscot Bionano scaffolding correction tool 9
biscot
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1.1 bp_genbank2gff3 Converts GenBank format files to GFF3 Genomics Software engineering Data management Data handling Service invocation 83704
perl-bioperl
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2.1.15 biom_add_metadata biom_convert biom_from_uc biom_normalize_table biom_subset_table biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. Laboratory information management Sequence analysis Formatting 62645
biom-format
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0.1.0 fasta_regex_finder Miscellanea of scripts for bioinformatics 8076
python
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0.21.9 bioext_bam2msa bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! 148530
python-bioext
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1.4.3 bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. Metagenomics Sequence assembly Microbial ecology Read binning Sequence clustering 483
binning_refiner
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1.1.1 binette Binning refinement tool Metagenomics Read binning 0
binette
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0.2.4 bigwig_outlier_bed pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files 4692
python
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1.1.9 bigscape Construct sequence similarity networks of BGCs and groups them into GCF Phylogeny Microbial ecology Mapping Metabolomics Bioinformatics Gene and protein families Clustering Global alignment Fold recognition 3588
bigscape
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0.2.3 berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. 3072
berokka
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1.0 bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. 11397
bellerophon
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0.0.2 bellavista_prepare Open-Source Visualization for Imaging-Based Spatial Transcriptomics 0
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2.31.1 bedtools_annotatebed bedtools_bamtobed bedtools_bed12tobed6 bedtools_bedtobam bedtools_bedtoigv bedtools_bedpetobam bedtools_closestbed bedtools_clusterbed bedtools_complementbed bedtools_coveragebed bedtools_expandbed bedtools_fisher bedtools_flankbed bedtools_genomecoveragebed bedtools_getfastabed bedtools_groupbybed bedtools_intersectbed bedtools_jaccard bedtools_links bedtools_makewindowsbed bedtools_map bedtools_maskfastabed bedtools_mergebed bedtools_multicovtbed bedtools_multiintersectbed bedtools_nucbed bedtools_overlapbed bedtools_randombed bedtools_reldistbed bedtools_shufflebed bedtools_slopbed bedtools_sortbed bedtools_spacingbed bedtools_subtractbed bedtools_tagbed bedtools_unionbedgraph bedtools_windowbed bedtools is a powerful toolset for genome arithmetic Genomics Mapping 4674820
bedtools
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2.4.42 bedops-sort-bed BEDOPS: high-performance genomic feature operations 1371
bedops
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5.4_29Oct24.c8e beagle Beagle is a program for phasing and imputing missing genotypes. 411
beagle
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2.0.0 beacon2_csv2xlsx beacon2_pxf2bff beacon2_vcf2bff beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). Genetic variation Population genetics Data security Rare diseases Service discovery Database search Genetic variation analysis 156
beacon2-ri-tools
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2.2.4 beacon2_analyses beacon2_biosamples beacon2_bracket beacon2_cnv beacon2_cohorts beacon2_datasets beacon2_gene beacon2_import beacon2_individuals beacon2_range beacon2_runs beacon2_sequence Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants. Genetic variation Population genetics Data security Rare diseases Service discovery Database search Genetic variation analysis 153
beacon2-import
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0.2.2 bctools_convert_to_binary_barcode bctools_extract_crosslinked_nucleotides bctools_extract_alignment_ends bctools_extract_barcodes bctools_merge_pcr_duplicates bctools_remove_tail bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 7086
bctools
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1.15.1 bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@_from_vcf bcftools_@EXECUTABLE@_to_vcf bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@_list_samples bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ BCFtools toolkit wrappers Genetic variation DNA polymorphism GWAS study Genotyping experiment Data handling Variant calling 0
bcftools
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39.08 bbtools_bbduk bbtools_bbmap bbtools_bbmerge bbtools_bbnorm bbtools_callvariants bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. Sequencing RNA splicing Whole genome sequencing Phylogenetics Metagenomics RNA-Seq RNA-Seq analysis Sequence trimming Read mapping Sequence contamination filtering Read binning Sequence alignment 78030
bbmap
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0.1 bbgtobigwig Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file. Sequence analysis 3246
ucsc-bedgraphtobigwig
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2.1 BayeScan Detecting natural selection from population-based genetic data Genetics Evolutionary biology Statistics and probability DNA polymorphism Statistical inference 312
bayescan
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0.0.11 bax2bam BAX to BAM converter 1152
bax2bam
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1.2.0 basil Breakpoint detection, including large insertions 2340
anise_basil
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1.2.2 barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. Genomics Model organisms Model organisms Gene prediction 46266
barrnap
To update
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1.1.3 baredsc_1d baredsc_2d baredsc_combine_1d baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. RNA-Seq Cytometry Transcriptomics Gene transcripts Statistics and probability Data retrieval Expression correlation analysis Differential gene expression profiling 945
baredsc
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0.18.4.0 barcode_splitter A utility to split sequence files using multiple sets of barcodes 0
barcode_splitter
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2022.09 bandage_image bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily Genomics Sequence assembly Sequence assembly visualisation 452197
bandage_ng
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bamutil_clip_overlap bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. 1308
bamutil
To update
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1.0.1 bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. 1605
openjdk
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1.9.4 bakta "Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis." Genomics Sequence analysis Bioinformatics Genome annotation 117156
bakta
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3.0.5+galaxy0 b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. Protein disorder prediction Protein secondary structure prediction Protein feature detection 1116
b2btools
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0.6.2 autobigs-cli Automated MLST typing from PubMLST and InstitutPasteur. 0
autobigs-cli
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3.4.0 augustus augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. Gene transcripts Gene and protein families Gene prediction Ab-initio gene prediction Homology-based gene prediction Homology-based gene prediction Operation 134444
augustus
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5.7.8 astral Tool for estimating an unrooted species tree given a set of unrooted gene trees 453
astral-tree
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17.02 assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. 78
rjchallis-assembly-stats
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1.6.0 artic_guppyplex artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building Genomics Sequence alignment 37329
artic
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art
2014.11.03.0 art_454 art_illumina art_solid Simulator for Illumina, 454, and SOLiD sequencing data Bioinformatics Conversion 777
art
art
To update
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2.5.0 arriba arriba_draw_fusions arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR 12948
arriba
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1.0.0 argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database Gene functional annotation 228
argnorm
Up-to-date
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3.18.0 annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages Annotation 310497
bioconductor-org.hs.eg.db
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1.3.2 anndata2ri Convert between Anndata and SingCellExperiment objects Data handling 0
anndata2ri
Up-to-date
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0.10.9 anndata_export anndata_import anndata_inspect anndata_manipulate modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects 230553
anndata
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1.4.0 ancombc Performs analysis of compositions of microbiomes with bias correction. Microbial ecology Metagenomics Taxonomy DNA barcoding 111
bioconductor-ancombc
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3.12.8 amrfinderplus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms. Microbiology Public health and epidemiology Infectious disease Antimicrobial resistance prediction 57534
ncbi-amrfinderplus
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2.8.9 ampvis2_alpha_diversity ampvis2_boxplot ampvis2_core ampvis2_export_fasta ampvis2_export_otu ampvis2_frequency ampvis2_heatmap ampvis2_load ampvis2_merge_ampvis2 ampvis2_mergereplicates ampvis2_octave ampvis2_ordinate ampvis2_otu_network ampvis2_rankabundance ampvis2_rarecurve ampvis2_setmetadata ampvis2_subset_samples ampvis2_subset_taxa ampvis2_timeseries ampvis2_venn ampvis2 Biodiversity Analysis Visualisation 8136
To update
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1.14.0 amplican AmpliCan is an analysis tool for genome editing. PCR experiment Statistics and probability Alignment Standardisation and normalisation 252
bioconductor-amplican
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2 allegro Linkage and haplotype analysis from deCODE Sequence analysis Transcription factors and regulatory sites DNA Sequence motif discovery 0
allegro
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1.26.0 aldex2 Performs analysis Of differential abundance taking sample variation into account Gene expression Statistics and probability Statistical inference 897
bioconductor-aldex2
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0.16.0 aegean_canongff3 aegean_gaeval aegean_locuspocus aegean_parseval AEGeAn toolkit wrappers Sequence analysis Gene structure Sequence annotation 7857
aegean
Up-to-date
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0.2.0 addName Add input name as column on an existing tabular file 341288
python
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2.3.4 adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. Sequence trimming Sequence merging Primer removal 1551
adapterremoval
Up-to-date
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2.3.10 abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler Sequence assembly Genome assembly De-novo assembly Scaffolding 28259
abyss
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1.0.19 abritamr A pipeline for running AMRfinderPlus and collating results into functional classes Microbiology Public health and epidemiology Infectious disease Antimicrobial resistance Antimicrobial resistance prediction 4989
abritamr
Up-to-date
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1.0.1 abricate abricate_list abricate_summary Mass screening of contigs for antiobiotic resistance genes Genomics Microbiology Antimicrobial resistance prediction 4634468
abricate
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0.1.0 trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline 144
trimns_vgp
To update
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0.1.2 venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc 54544
galaxy_sequence_utils
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0.0.15 seq_select_by_id Select sequences by ID 9805
biopython
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0.0.10 seq_rename Rename sequences with ID mapping from a tabular file 0
galaxy_sequence_utils
To update
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0.0.18 seq_primer_clip Trim off 5' or 3' primers 0
galaxy_sequence_utils
To update
0.0.5 seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) 0
biopython
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0.0.8 seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files 13558
biopython
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0.2.9 seq_filter_by_id Filter sequences by ID 206407
biopython
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0.0.5 seq_composition Sequence composition 6218
biopython
To update
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0.0.6 samtools_idxstats BAM mapping statistics (using samtools idxstats) 515441
samtools
To update
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0.0.3 samtools_depth Coverage depth via samtools 55812
samtools
To update
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0.0.5 samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) 0
samtools
To update
0.2.6 sample_seqs Sub-sample sequences files (e.g. to reduce coverage) 20847
biopython
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0.0.13 promoter2 Psortb rxlr_motifs signalp3 tmhmm2 wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb 38351
promoter
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0.0.10 predictnls Python reimplementation of predictNLS for Galaxy 0
To update
0.0.11 nlstradamus Find nuclear localization signals (NLSs) in protein sequences 0
NLStradamus
To update
0.0.8 mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot 5866
ghostscript
To update
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0.2.3 get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) 8038
biopython
To update
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0.1.5 fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads 0
galaxy_sequence_utils
To update
0.0.5 fastq_pair_names Extract FASTQ paired read names 0
galaxy_sequence_utils
To update
0.0.7 fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) 0
galaxy_sequence_utils
To update
0.0.7 fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) 0
galaxy_sequence_utils
To update
0.0.21 effectiveT3 Find bacterial type III effectors in protein sequences Sequence analysis Sequence classification 0
effectiveT3
To update
0.1.0 coverage_stats BAM coverage statistics using samtools idxstats and depth 0
samtools
To update
UseGalaxy.fr1
0.0.6 count_roi_variants Count sequence variants in region of interest in BAM file 0
samtools
To update
UseGalaxy.fr1
0.1.0 clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins Sequence analysis Nucleic acid sequence analysis 1677
clinod
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UseGalaxy.or1
0.0.7 clc_assembler clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio 0
samtools
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0.0.3 chromosome_diagram Chromosome Diagrams using Biopython 0
biopython
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0.0.10 align_back_trans Thread nucleotides onto a protein alignment (back-translation) 1700
biopython
To update
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2.5 wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. Sequence assembly Sequencing Genome assembly De-novo assembly 4996
wtdbg
Up-to-date
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1.9.4 wordcloud A little word cloud generator in Python. 36
wordcloud
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20231117 whisper Transcribe audio or video files to text using the OpenAI Whisper. 702
To update
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vt
0.2 vt_@BINARY@ vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. 0
vt
To update
0.6 uniprot UniProt ID mapping and sequence retrieval 21429
requests
To update
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0.6.7 trim_galore Trim Galore adaptive quality and adapter trimmer Sequence analysis Sequence trimming Primer removal Read pre-processing 1861714
trim-galore
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0.0.5 create_tool_recommendation_model Create model to recommend tools 1332
python
To update
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1.0.3 tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. Sequencing Genomics DNA polymorphism DNA structural variation Genome comparison Data retrieval Variant calling Genome visualisation Structural variation detection 888
tiara
To update
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1.0.3 tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. Sequencing Sequence assembly Phylogeny Transcription factors and regulatory sites Mapping Genome assembly Read mapping Scaffolding Localised reassembly 1656
tgsgapcloser
To update
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9.5 tp_awk_tool tp_cat tp_cut_tool tp_easyjoin_tool tp_find_and_replace tp_grep_tool tp_head_tool tp_multijoin_tool nl tp_text_file_with_recurring_lines tp_replace_in_column tp_replace_in_line tp_sed_tool tp_sort_header_tool tp_sort_rows tp_uniq_tool tp_tac tp_tail_tool tp_unfold_column_tool tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. 15244959
coreutils
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0.5.2 split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. 102357
python
To update
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0.6 tp_split_on_column Split a file on a specific column. 28075
gawk
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1.0.1 join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. 10007
python
To update
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0.2 bg_column_arrange_by_header Column arrange by header name 33993
To update
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0.1.0 add_line_to_file Adds a text line to the beginning or end of a file. 60705
coreutils
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4.76+galaxy0 tapscan_classify Search for transcription associated proteins (TAPs) 114
hmmer
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2.0.3 tabpfn Tabular data prediction using TabPFN using Pytorch. 219
tabpfn
To update
UseGalaxy.eu1
0.12.04 stress_ng stress test a computer system in various selectable ways 186
stress-ng
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0.3 bg_statistical_hypothesis_testing Tool for computing statistical tests. 733
numpy
To update
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0.5.0 rbc_splitfasta Split a multi-sequence fasta file into files containing single sequences 18312
biopython
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1.0.11.0 sklearn_mlxtend_association_rules sklearn_clf_metrics sklearn_discriminant_classifier sklearn_ensemble sklearn_estimator_attributes sklearn_feature_selection sklearn_fitted_model_eval sklearn_generalized_linear keras_batch_models keras_model_builder keras_model_config keras_train_and_eval sklearn_label_encoder sklearn_lightgbm ml_visualization_ex model_prediction sklearn_model_validation sklearn_nn_classifier sklearn_numeric_clustering sklearn_pairwise_metrics sklearn_pca sklearn_build_pipeline sklearn_data_preprocess sklearn_regression_metrics sklearn_sample_generator sklearn_searchcv sklearn_model_fit scipy_sparse stacking_ensemble_models sklearn_svm_classifier sklearn_to_categorical sklearn_train_test_eval sklearn_train_test_split Machine Learning tool suite from Scikit-learn 358069
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0.2.0.4 segemehl segemehl - short read mapping with gaps 3310
segemehl
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0.0.1 sed_stream_editor Manipulate your data with the sed command line tool. 2514
sed
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1.0.1 sambamba_flagstat sambamba_markdup sambamba_merge sambamba_sort Sambamba: process your BAM data faster! 8142
sambamba
Up-to-date
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1.10.1 alevin salmon salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. RNA-Seq Gene expression Transcriptomics Sequence composition calculation RNA-Seq quantification Gene expression analysis 606991
salmon
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0.10.1.1 sailfish Sailfish is a tool for transcript quantification from RNA-seq data 53925
bzip2
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2.2.10 viennarna_kinfold viennarna_kinwalker viennarna_rna2dfold viennarna_rnaaliduplex viennarna_rnaalifold viennarna_rnacofold viennarna_rnadistance viennarna_rnaduplex viennarna_rnaeval viennarna_rnafold viennarna_rnaheat viennarna_rnainverse viennarna_rnalalifold viennarna_rnalfold viennarna_rnapaln viennarna_rnadpdist viennarna_rnapkplex viennarna_rnaplex viennarna_rnaplfold viennarna_rnaplot viennarna_rnasnoop viennarna_rnasubopt viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures 14087
viennarna
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0.6 aragorn_trna trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. 23905
aragorn
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1.7 targetfinder Plant small RNA target prediction tool 6594
targetfinder
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1.0.7 sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data 623
sshmm
Up-to-date
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4.3.6 bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. Metatranscriptomics Metagenomics Sequence similarity search Sequence comparison Sequence alignment analysis 92904
sortmerna
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1.0.5 selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format 1017
selectsequencesfrommsa
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2.1.1 rnaz rnaz_annotate rnaz_cluster rnaz_randomize_aln rnaz_select_seqs rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. 45487
rnaz
Up-to-date
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1.2.0 rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs 221
rnasnp
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1.3.6 RNAlien RNAlien unsupervized RNA family model construction 77
rnalien
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1.2.0 infer_rnaformer RNAformer: RNA secondary structure prediction 228
rnaformer
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0.1.1 rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. 1188
sam
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0.3.2 rbc_rnacode Analyze the protein coding potential in MSA 3031
rnacode
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2.2.1.0 rbc_rnabob Fast pattern searching for RNA structural motifs 352
rnabob
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3.3.0 RNAshapes Compute secondary structures of RNA 684
@EXECUTABLE@
To update
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1.3.1a ribotaper_create_annotation ribotaper_create_metaplots ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. Functional genomics Gene expression profiling 2000
ribotaper
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1.0.0 remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation 172
remurna
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1.1 reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. Sequence assembly RNA Metagenomics Microbiology Sequence assembly 3
reago
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1.5.4 rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments 2871
bioconductor-rcas
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0.8.1 rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA Protein interactions RNA immunoprecipitation Bioinformatics Sequence analysis 327
rbpbench
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0.1 meta_rna Identification of ribosomal RNA genes in metagenomic fragments. 0
hmmsearch3.0
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0.1.0 pipmir A method to identify novel plant miRNA. 814
pipmir
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1.5 paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. 978
paralyzer
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1.0 nastiseq A method to identify cis-NATs using ssRNA-seq 98
r-nastiseq
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mqc
1.9 mqc Ribosome profiling mapping quality control tool 192
mqc
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mea
0.6.4.1 mea Maximum expected accuracy prediction 188
mea
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2.0.1 locarna_exparnap locarna_multiple locarna_pairwise locarna_pairwise_p locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs 992
locarna
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Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. 0
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3.4.1 intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. 13945
intarna
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INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. 0
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1.1.5 infernal_cmalign infernal_cmbuild infernal_cmpress infernal_cmscan infernal_cmsearch infernal_cmstat Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. Sequence sites, features and motifs Structural genomics Nucleic acid feature detection 230255
infernal
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0.1.0+galaxy0 htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets 318
htseq-clip
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1.1.7+galaxy2 graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. 1346
graphprot
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1.0.1 exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. 0
exparna
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1.3.1 dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence 208
vienna_rna
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5.7.a rnastructure_dot2ct Dot-Bracket to Connect Table (CT) 0
rnastructure
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1.0 dorina_search data source for RNA interactions in post-transcriptional regulation 3173
To update
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0.1.0+galaxy0 dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data 288
python
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2.1.1 coprarna Target prediction for prokaryotic trans-acting small RNAs 0
coprarna
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1.0 compalignp Compute fractional identity between trusted alignment and test alignment 280
compalignp
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2.0.4.0 cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. 875
cofold
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cmv
1.0.8 cmcv cmv hmmcv hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. 254
cmv
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0.08+galaxy2 cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. Biology Medicine Comparison Alignment 8946
perl
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1.1.1 blockclust BlockClust detects transcripts with similar processing patterns. 5306
blockclust
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0.1.2 AREsite2_REST AREsite2 REST Interface 180
python
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1.1 antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . 874
antarna
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0.1.0 pubchem_rest_tool This tool fetches data from pubchem via the PubChem REST API. 0
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0.2 replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. 1876346
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0.1.2 repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. 64172
RepeatMasker
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1.5.0 racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Whole genome sequencing Sequence assembly Genome assembly Mapping assembly 159700
racon
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2022.11.1+galaxy0 qiime2_dbotu_q2 q2-dbotu is a Qiime 2 plugin for performing OTU clustering Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 0
To update
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1.1.0.1 proteomics_improviser Visualisation of PepXML files 0
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0.2.0 bg_protein_properties Calculation of various properties from given protein sequences 1682
biopython
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0.9 eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. 370
eden
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0.1 plotly_regression_performance_plots performance plots for regression problems 4710
python
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0.2 plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly 4992
python
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0.4 plotly_ml_performance_plots performance plots for machine learning problems 10391
galaxy-ml
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0.0.11 bg_platypus efficient and accurate variant-detection in high-throughput sequencing data 0
platypus
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1.2.1.0 piranha Piranha is a peak-caller for CLIP- and RIP-Seq data 4624
piranha
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pharmcat Pharmacogenomics Clinical Annotation Tool 1296
To update
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pg_dump pg_import pg_query tool suite for dealing with Postgresql databases from Galaxy's history 0
postgresql
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1.6 pfamscan Search a FASTA sequence against a library of Pfam HMM. Sequence analysis Protein sequence analysis 6141
pfam_scan
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5.11.0 stats_perf_tool suitable for boolean classification problems 0
perf
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0.2.0+galaxy1 peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data 8916
peakachu
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0.1 pandas_rolling_window Rolling window calculations 922
numpy
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2.1.0 AccurateMassSearch AdditiveSeries BaselineFilter CVInspector CompNovo CompNovoCID ConsensusID ConsensusMapNormalizer ConvertTSVToTraML ConvertTraMLToTSV DTAExtractor DeMeanderize Decharger DecoyDatabase Digestor DigestorMotif EICExtractor ERPairFinder ExternalCalibration FFEval FalseDiscoveryRate FeatureFinderCentroided FeatureFinderIdentification FeatureFinderIsotopeWavelet FeatureFinderMRM FeatureFinderMetabo FeatureFinderMultiplex FeatureFinderSuperHirn FeatureLinkerLabeled FeatureLinkerUnlabeled FeatureLinkerUnlabeledQT FidoAdapter FileConverter FileFilter FileInfo FileMerger FuzzyDiff HighResPrecursorMassCorrector IDConflictResolver IDDecoyProbability IDExtractor IDFileConverter IDFilter IDMapper IDMassAccuracy IDMerger IDPosteriorErrorProbability IDRTCalibration IDRipper IDScoreSwitcher IDSplitter ITRAQAnalyzer InclusionExclusionListCreator InspectAdapter InternalCalibration IsobaricAnalyzer LabeledEval LowMemPeakPickerHiRes LowMemPeakPickerHiRes_RandomAccess LuciphorAdapter MRMMapper MRMPairFinder MRMTransitionGroupPicker MSGFPlusAdapter MSSimulator MapAlignmentEvaluation MapNormalizer MapRTTransformer MapStatistics MascotAdapter MascotAdapterOnline MassCalculator MassTraceExtractor MetaProSIP MetaboliteSpectralMatcher MultiplexResolver MzMLSplitter MzTabExporter NoiseFilterGaussian NoiseFilterSGolay OpenSwathAnalyzer OpenSwathAssayGenerator OpenSwathChromatogramExtractor OpenSwathConfidenceScoring OpenSwathDIAPreScoring OpenSwathDecoyGenerator OpenSwathFeatureXMLToTSV OpenSwathFileSplitter OpenSwathMzMLFileCacher OpenSwathRTNormalizer OpenSwathRewriteToFeatureXML OpenSwathWorkflow PTModel PTPredict PeakPickerHiRes PeakPickerIterative PeakPickerWavelet PepNovoAdapter PeptideIndexer PhosphoScoring PrecursorIonSelector PrecursorMassCorrector ProteinInference ProteinQuantifier ProteinResolver QCCalculator QCEmbedder QCExporter QCExtractor QCImporter QCMerger QCShrinker RNPxl RNPxlXICFilter RTEvaluation RTModel RTPredict SemanticValidator SequenceCoverageCalculator SimpleSearchEngine SpecLibCreator SpectraFilterBernNorm SpectraFilterMarkerMower SpectraFilterNLargest SpectraFilterNormalizer SpectraFilterParentPeakMower SpectraFilterScaler SpectraFilterSqrtMower SpectraFilterThresholdMower SpectraFilterWindowMower SpectraMerger SvmTheoreticalSpectrumGeneratorTrainer TICCalculator TMTAnalyzer TOFCalibration TextExporter TopPerc TransformationEvaluation XMLValidator XTandemAdapter OpenMS in version 2.1. 182889
openms
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0.9 numeric_clustering Clustering tool for numberic values 1008
anaconda
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3.0 Nucleosome Prediction of Nucleosomes Positions on the Genome Structural genomics Nucleic acid sites, features and motifs Prediction and recognition Nucleosome position prediction Sequence analysis 1019
nucleosome_prediction
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2.5.0 nextdenovo String graph-based de novo assembler for long reads Sequencing Sequence assembly De-novo assembly Genome assembly 1629
nextdenovo
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1.6.0 netboxr netboxr enables automated discovery of biological process modules by network analysis 39
bioconductor-netboxr
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0.14.0 nanopolish_eventalign nanopolish_methylation nanopolish_polya nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. 35655
nanopolish
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0.1.1 music_construct_eset music_inspect_eset music_manipulate_eset music_compare music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) 18753
music-deconvolution
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3.1.0 mereg_mOTUs_tables motus_profiler Tool for profiling the abundance of microbial taxa. Metagenomics Taxonomic classification 228
motus
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0.2 bg_mol2gspan converter 0
openbabel
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3 mitohifi Assembly mitogenomes from Pacbio HiFi read. 7653
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0.1.3 minipolish Polishing miniasm assemblies Sequence assembly Sequencing Localised reassembly Read depth analysis 753
minipolish
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0.2.0 minced MinCED - Mining CRISPRs in Environmental Datasets 5700
minced
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1.2.0 mi_clip Identification of binding sites in CLIP-Seq data. 0
Rscript
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1.2 mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. Genomics Sequence assembly Sequencing Probes and primers Nucleic acid design 3762
To update
UseGalaxy.or1
0.2.6.1 metilene Differential DNA methylation calling 14623
metilene
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0.99.2 methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. 21
bioconductor-methylkit
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UseGalaxy.fr1
0.5.2 pileometh A tool for processing bisulfite sequencing alignments 74796
methyldackel
To update
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0.1.1 methtools_calling r_correlation_matrix methtools_destrand methtools_dmr methtools_filter methtools_plot smooth_running_window methtools_tiling tools for methylation analysis 6521
methtools
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0.9 mavedb_importer data source for MaveDB 30
To update
UseGalaxy.eu1
0.1.1 markitdown Convert documents to Markdown using markitdown 0
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7.526 rbc_mafft_add rbc_mafft Multiple alignment program for amino acid or nucleotide sequences Sequence analysis Multiple sequence alignment 997972
mafft
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1.0 lighter Lighter is a kmer-based error correction method for whole genome sequencing data Sequencing Whole genome sequencing DNA Genomics k-mer counting Sequence read processing Sequencing quality control Sequencing error detection 468
lighter
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1.0.5.0 bg_labels remaps and annotates alignments 0
labels
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0.0.1 run_jupyter_job Run jupyter notebook script in Galaxy 99
To update
2.17.0 jbrowse2 JBrowse2 Genome Browser integrated as a Galaxy Tool Mapping Structural variation Genomics Gene structure Sequence assembly Genome visualisation Structure visualisation Pathway visualisation 8772
jbrowse2
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1.1.3 itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. Functional, regulatory and non-coding RNA Microbiology Sequence feature detection 6705
itsx
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Interproscan queries the interpro database and provides annotations. 0
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0.1.6 instagraal Large genome reassembly based on Hi-C data Sequence assembly Mapping Metagenomics Statistics and probability DNA binding sites Genome assembly Mapping assembly Genetic mapping Scaffolding 477
To update
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1.6.1 woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays 93
fiji-morpholibj
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20240614 imagej2_adjust_threshold_binary imagej2_analyze_particles_binary imagej2_analyze_skeleton imagej2_binary_to_edm imagej2_bunwarpj_adapt_transform imagej2_bunwarpj_align imagej2_bunwarpj_compare_elastic imagej2_bunwarpj_compare_elastic_raw imagej2_bunwarpj_compare_raw imagej2_bunwarpj_compose_elastic imagej2_bunwarpj_compose_raw imagej2_bunwarpj_compose_raw_elastic imagej2_bunwarpj_convert_to_raw imagej2_bunwarpj_elastic_transform imagej2_bunwarpj_raw_transform imagej2_create_image imagej2_crop imagej2_enhance_contrast imagej2_filter imagej2_find_edges imagej2_find_maxima imagej2_make_binary imagej2_math imagej2_noise imagej2_shadows imagej2_sharpen imagej2_skeletonize3d imagej2_smooth imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. Imaging Image analysis Image annotation Visualisation 4442
imagej2
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UseGalaxy.cz27 UseGalaxy.eu27 UseGalaxy.no27
1.3.45 graphicsmagick_image_compare graphicsmagick_image_convert graphicsmagick_image_montage Contains tools based on GraphicsMagick 6092
graphicsmagick
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0.2.0 bia_download Tool to query ftp links for study from bioimage archive 39
wget
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UseGalaxy.eu1
0.1 illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays 0
Rscript
To update
Software for motif discovery and next generation sequencing analysis. 0
To update
0.9.2 hicup2juicer hicup_deduplicator hicup_digester hicup_filter hicup_hicup hicup_mapper hicup_truncater The HiCUP-Pipeline from the Bioinformatics Babraham Institute. 4870
To update
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2.0.2 hictk Convert cooler to juicebox_hic 153
hictk
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0.99 hclust2 Plots heatmaps 0
hclust2
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0.5.2 graphmap_align graphmap_overlap Mapper for long, error-prone reads. Gene transcripts RNA-Seq RNA splicing Sequence trimming EST assembly Read mapping 20966
graphmap
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0.1 graphclust GraphClust can be used for structural clustering of RNA sequences. 6
GraphClust
To update
0.1.0 graph_converter Convert between different graph formats 0
To update
1.3.0 rbc_gotohscan Find subsequences in db 124
gotohscan
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GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) 0
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1.3.10 gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. Computational biology Data handling 78345
gfastats
Up-to-date
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0.2.0 format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels Taxonomy Metagenomics Formatting 19244
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1.0.0+galaxy1 format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file 682
To update
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1.0.0 footprint Find transcription factor footprints 171
footprint
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2.9.5 flye Assembly of long and error-prone reads. Sequence assembly Metagenomics Whole genome sequencing Genomics Genome assembly De-novo assembly Mapping assembly Cross-assembly 227846
flye
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2024 black_forest_labs_flux Using the black forest labs FLUX.1 models to generate image based on user input. 297
To update
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0.2.17 flexynesis flexynesis_cbioportal_import This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. 39
flexynesis
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0.3 bg_find_subsequences 11412
biopython
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0.4 bg_uniq This tool returns all unique lines from a tab-separated file. 22467
python
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0.1.0 ffmpeg_converter A complete, cross-platform solution to record, convert and stream audio and video. 0
ffmpeg
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0.25.1 fastq_info FASTQ info allows to validate single or paired fastq files 70647
fastq_utils
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@VERSION_STRING@ epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. 525
epicseg
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edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Workflows Mobile genetic elements Plant biology Transcription factors and regulatory sites Model organisms De-novo assembly Deisotoping Genome annotation 13803
edta
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24.10.15 make_ear A tool to compile assembly reports and stastics from assembly pipeline 249
reportlab
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Diffbind provides functions for processing ChIP-Seq data. 0
To update
3.10 diff GNU diff tool that calculates the differences between two files. 1323
diffutils
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1.2.0 crispr_recognition_tool CRISPR Recognition Tool 13229
crisper_recognition_tool
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3.0.5 cpat Coding-potential assessment tool using an alignment-free logistic regression model. 2097
cpat
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0.2.0 compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information Metagenomics Gene and protein families Comparison 902
To update
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0.3.0 combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances Metagenomics Molecular interactions, pathways and networks Aggregation 1929
python
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1.1.9.0 circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) 1344
circexplorer
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1.32.0 chipseeker A tool for ChIP peak annotation and visualization 177827
bioconductor-chipseeker
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2024 chatgpt_openai_api Using the OpenAI GPT models to generate text based on user input. 1638
python
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4.2.8 cp_cellprofiler4 cellProfiler4 wrapper 165
To update
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cp_cellprofiler cp_color_to_gray cp_convert_objects_to_image cp_display_data_on_image cp_enhance_or_suppress_features cp_export_to_spreadsheet cp_gray_to_color cp_identify_primary_objects cp_image_math cp_mask_image cp_measure_granularity cp_measure_image_area_occupied cp_measure_image_intensity cp_measure_image_quality cp_measure_object_intensity cp_measure_object_size_shape cp_measure_texture cp_overlay_outlines cp_relate_objects cp_save_images cp_common cp_tile cp_track_objects cellProfiler wrapper Imaging Microarray experiment Genotype and phenotype Quantification Image analysis Parsing 35586
cellprofiler
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3.1.0 cellpose Cellpose is an anatomical segmentation algorithm 66
To update
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2.2 canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). Genomics De-novo assembly 54832
canu
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0.1.2 blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. 5538
blockbuster
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4.0.7 blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. 7989
To update
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0.22.1 bismark_pretty_report bismark_bowtie2 bismark_deduplicate bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states 48876
bismark
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3.7.0 bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data 4305
To update
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1.1 biomodels_biomd0000001066 biomodels_biomd0000001076 Wrappers for tools to bring BioModels AI models into Galaxy. 339
To update
UseGalaxy.eu2
2.4.1 bioimage_inference Load model from BioImage.IO and make inferences Machine learning Computer science 177
python
pytorch
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0.1.0 bigwig_to_bedgraph Convert from bigWig to bedGraph format 21347
ucsc_tools
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0.1.0 barcode_collapse Paired End randomer aware duplicate removal algorithm 0
pysam
To update
1.1 bamhash Hash BAM and FASTQ files to verify data integrity 456
bamhash
Up-to-date
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0.1.6 atactk_trim_adapters Trim adapters from paired-end HTS reads. 737
atactk
To update
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6.1.1 antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters Molecular interactions, pathways and networks Gene and protein families Sequence clustering Gene prediction Differential gene expression analysis 120907
antismash
To update
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1.4.0 agat GTF/GFF analysis toolkit Genomics Data handling Genome annotation 19113
agat
To update
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0.4 structure_to_gspan Convert RNA structure to GSPAN graphs 4768
graphclust-wrappers
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0.5 preproc Preprocessing input for GraphClust 3825
graphclust-wrappers
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0.4 preMloc This tool prepares files for locarna step. 4064
graphclust-wrappers
To update
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0.4 motifFinderPlot Plotting results for GraphClust 143
seaborn
To update
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9.2.3.1 NSPDK_candidateClust nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. 68077
graphclust-wrappers
To update
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0.4 locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. 97439
graphclust-wrappers
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0.4 gspan Second step of GraphClust 325
graphclust-wrappers
To update
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0.5 graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. 162
graphclust-wrappers
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
0.5 glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. 3893
graphclust-wrappers
To update
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0.4 cmFinder Determines consensus motives for sequences. 97239
graphclust-wrappers
To update
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0.1 graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. 3429
graphclust-wrappers
To update
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0.6.0 graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. 196
graphclust-wrappers
Up-to-date
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1.4.1 10x_bamtofastq Converts 10x Genomics BAM to FASTQ 1101
10x_bamtofastq
Up-to-date
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0.1 vcftools_subset Select samples from a VCF dataset 744
tabix
To update
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0.1 vcftools_slice Subset VCF dataset by genomic regions 20496
echo
To update
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0.1.11 vcftools_merge Merge multiple VCF datasets into a single dataset 3892
tabix
To update
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0.1.1 vcftools_isec Intersect multiple VCF datasets 1963
tabix
To update
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0.1.11 vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence 0
samtools
To update
UseGalaxy.fr1
0.1 vcftools_compare Compare VCF files to get overlap and uniqueness statistics 1583
tabix
To update
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0.1 vcftools_annotate Annotate VCF using custom/user-defined annotations 9161
echo
To update
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1.0.0 t2t_report Summarize taxonomy 10238
taxonomy
To update
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1.0.0 Draw_phylogram Draw phylogeny Phylogenomics Phylogenetic tree visualisation 9456
taxonomy
To update
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1.0.0 poisson2test Poisson two-sample test 1920
taxonomy
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1.0.1 lca1 Find lowest diagnostic rank 6633
taxonomy
To update
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1.2+galaxy0 Kraken2Tax Convert Kraken output to Galaxy taxonomy data. 185332
gawk
To update
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1.1.1 Fetch Taxonomic Ranks Fetch taxonomic representation Taxonomy Database search ID mapping 15961
taxonomy
To update
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1.0.0 find_diag_hits Find diagnostic hits 1965
taxonomy
To update
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1.0.1 hgv_snpFreq snpFreq significant SNPs in case-control data 2058
R
To update
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1.0.0 hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve 499
R
To update
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1.0.0 hgv_funDo FunDO human genes associated with disease terms 2002
To update
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1.0.0 tables_arithmetic_operations Arithmetic Operations on tables 6728
perl
To update
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0.1 subtract_query1 Subtract Whole Dataset from another dataset 53255
bx-python
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1.0.0 gops_subtract_1 Subtract the intervals of two datasets 2050538
bx-python
To update
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1.0.0 gops_merge_1 Merge the overlapping intervals of a dataset 1964677
bx-python
To update
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1.0.0 gops_join_1 Join the intervals of two datasets side-by-side 975954
bx-python
To update
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1.0.0 gops_intersect_1 Intersect the intervals of two datasets 1289032
bx-python
To update
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1.0.0 get_flanks1 Get flanks returns flanking region/s for every gene 595713
bx-python
To update
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4.0.1 flanking_features_1 Fetch closest non-overlapping feature for every interval 43133
bx-python
To update
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1.0.0 gops_coverage_1 Coverage of a set of intervals on second set of intervals 57619
bx-python
To update
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1.0.1 gops_concat_1 Concatenate two bed files 1966123
bx-python
To update
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1.0.0 gops_complement_1 Complement intervals of a dataset 7440
bx-python
To update
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1.0.0 gops_cluster_1 Cluster the intervals of a dataset 40618
bx-python
To update
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1.0.0 gops_basecoverage_1 Base Coverage of all intervals 51531
bx-python
To update
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1.0.2 XY_Plot_1 Plotting tool for multiple series and graph types 51540
r-base
To update
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1.0.1 winSplitter Make windows 4282
bx-python
To update
UseGalaxy.or1
1.0.1 wtavg Assign weighted-average of the values of features overlapping an interval 2684
galaxy-ops
To update
UseGalaxy.or1
1.0.0 vcf_intersect Generate the intersection of two VCF files 1056
To update
UseGalaxy.fr1
1.0.0 vcf_filter Filter a VCF file 2486
To update
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1.0.0 vcf_extract Extract reads from a specified region 1435
To update
UseGalaxy.fr1
1.0.0 vcf_annotate Annotate a VCF file (dbSNP, hapmap) 782
To update
1.0.0 vcf2pgSnp VCF to pgSnp 6006
To update
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2.4.2 varscan VarScan wrapper 117577
varscan
To update
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1.0.1 build_ucsc_custom_track_1 Build custom track for UCSC genome browser 24735
python
To update
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0.0.1 trimmer Trim leading or trailing characters. 160128
To update
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0.1 tophat_fusion_post Wrapper for Tophat-Fusion post step 1803
blast+
To update
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2.1.1 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads 578428
bowtie2
To update
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1.5.0 tophat Tophat for Illumina 66771
samtools
To update
UseGalaxy.fr1
1.1.1 tab2fasta Tabular-to-FASTA 1546076
python
To update
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0.2 table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered 92519
annovar
To update
1.0.1 t_test_two_samples T Test for Two Samples 5753
R
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
1.0.1 substitutions1 Fetch substitutions from pairwise alignments 1049
bx-python
To update
UseGalaxy.or1
1.0.0 subRate1 Estimate substitution rates for non-coding regions 4393
To update
1.0.0 split_paired_reads Split paired end reads 677
To update
UseGalaxy.fr1
1.1 peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions 13544
SICER
Up-to-date
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1.0.0 Show tail1 Select lines from the end of a file. 53732
To update
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1.0.0 Show beginning1 Select lines from the beginning of a file. 385011
To update
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1.0.0 trim_reads Select high quality segments 7629
To update
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1.0.2 quality_score_distribution Build base quality distribution 4019
fontconfig
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
1.0.0 hist_high_quality_score Histogram of high quality score reads 0
rpy
To update
1.0.3 scatterplot_rpy Scatterplot of two numeric columns 15094
numpy
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
1.0.1 sam_bw_filter Filter SAM on bitwise flag values 82041
python
To update
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1.0.2 sam2interval Convert SAM to interval. 28033
python
To update
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1.0.0 rmapq_wrapper RMAPQ for Solexa Short Reads Alignment with Quality Scores 0
rmap
To update
1.0.0 rmap_wrapper RMAP for Solexa Short Reads Alignment 0
rmap
To update
1.0.0 Remove beginning1 Remove lines from the beginning of a file. 853432
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
1.0.0 rcve1 Compute RCVE 257
R
To update
UseGalaxy.or1
1.0.1 qualityFilter Filter nucleotides based on quality scores 880
bx-python
To update
1.0.2 pca1 Principal Component Analysis 43554
rpy
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
1.0.1 plot_for_lda_output1 Draw ROC plot on "Perform LDA" output 1704
R
To update
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1.0.2 pileup_parser Filter pileup on coverage and SNPs 88409
perl
To update
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1.0.3 pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases 14617
bx-python
To update
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1.0.0 pgSnp2gd_snp Convert from pgSnp to gd_snp 0
To update
1.0.0 Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns 2
To update
1.0.0 partialRsq Compute partial R square 214
R
To update
UseGalaxy.or1
1.0.0 mutate_snp_codon_1 Mutate Codons with SNPs 644
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
1.0.0 multispecies_orthologous_microsats Extract orthologous microsatellites 0
bx-sputnik
To update
0.0.1 maximal_information_based_nonparametric_exploration Maximal Information-based Nonparametric Exploration 127
MINE
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
1.1.0 microsats_mutability1 Estimate microsatellite mutability by specified attributes 385
bx-python
To update
UseGalaxy.or1
1.0.0 microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments 1214
sputnik
To update
UseGalaxy.or1
1.0.0 microsatellite_birthdeath Identify microsatellite births and deaths 0
To update
1.0.3 mergeCols1 Merge columns together. 264964
python
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
1.0.1 megablast_xml_parser Parse blast XML output 7725
python
To update
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1.0.0 mapToUCSC Format mapping data as UCSC custom track 0
To update
1.0.0 cpgFilter Mask CpG/non-CpG sites from MAF file 450
bx-python
To update
UseGalaxy.or1
1.0.1 LogisticRegression Perform Logistic Regression with vif 263
numpy
To update
1.0.1 LinearRegression1 Perform Linear Regression 1413
R
To update
UseGalaxy.or1
1.0.1 lda_analy1 Perform Linear Discriminant Analysis 3623
R
To update
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1.1.1 lastz_paired_reads_wrapper Galaxy wrapper for the Lastz alignment tool on paired reads 39
lastz
To update
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1.0.0 kpca1 Kernel Principal Component Analysis 1617
rpy
To update
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1.0.0 kcca1 Kernel Canonical Correlation Analysis 886
rpy
To update
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1.0.3 indels_3way Fetch Indels from 3-way alignments 386
To update
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1.0.5 histogram_rpy Histogram of a numeric column 77251
rpy2
To update
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1.0.3 hisat HISAT is a fast and sensitive spliced alignment program. 228
hisat
To update
UseGalaxy.fr1
2.0.1 gmaj_1 GMAJ Multiple Alignment Viewer 1210
To update
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1.0.0 getIndels_2way Fetch Indels from pairwise alignments 347
numpy
To update
UseGalaxy.or1
1.0.0 indelRates_3way Estimate Indel Rates for 3-way alignments 387
bx-python
To update
UseGalaxy.or1
1.0.0 generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA 3007
To update
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0.1 filter_combined_via_tracking Filter Combined Transcripts 812
To update
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2.0.0 featureCoverage1 Feature coverage 81300
bx-python
To update
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1.0.0 fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data 8
To update
1.1.5 fastq_quality_trimmer FASTQ Quality Trimmer by sliding window 184169
galaxy_sequence_utils
To update
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1.1.1 fasta2tab FASTA-to-Tabular converter 715337
python
To update
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1.2 fasta_filter_by_length Filter sequences by length 382565
python
To update
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0.0.1 fasta_concatenate0 Concatenate FASTA alignment by species 179237
bx-python
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1.0.4 fasta_compute_length Compute sequence length 137963
python
To update
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1.1.1 express Quantify the abundances of a set of target sequences from sampled subsequences 9793
eXpress
To update
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1.0.2 dwt_var1 Wavelet variance using Discrete Wavelet Transfoms 782
r-bitops
To update
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1.0.1 compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences 457
r-waveslim
To update
UseGalaxy.or1
1.0.1 compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences 428
r-waveslim
To update
UseGalaxy.or1
1.0.1 compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features 435
r-waveslim
To update
UseGalaxy.or1
1.0.1 compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences 476
r-waveslim
To update
UseGalaxy.or1
1.0.0 draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria 1231
R
To update
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1.0.0 dividePgSnp Separate pgSnp alleles into columns 396
To update
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0.1 dgidb_annotate Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) 477
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
1.0.0 delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file 92
To update
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1.0.2 Cut1 Select columns from a dataset. 8073071
To update
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1.0.1 cummerbund_to_cuffdiff Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. 6935
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
2.16.0 cummeRbund Wrapper for the Bioconductor cummeRbund library 33480
fonts-conda-ecosystem
To update
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1.0.0 ctdBatch_1 CTD analysis of chemicals, diseases, or genes 1032
To update
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0.2 count_gff_features Count GFF Features 5477
galaxy-ops
To update
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1.0.0 cor2 Correlation for numeric columns 8627
rpy
To update
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1.0.0 color2nuc Convert Color Space to Nucleotides 0
To update
1.0.1 Convert characters1 Convert delimiters to tab. 318302
python
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
1.0.0 Condense characters1 Condense consecutive characters. 2889
To update
UseGalaxy.fr1 UseGalaxy.or1
1.0.1 compute_q_values Compute q-values based on multiple simultaneous tests p-values 35
R
To update
1.0.0 compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. 1176
To update
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1.0.0 compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. 1270
To update
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1.0.1 ChangeCase Convert column case. 80242
perl
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0.0.1 cd_hit_dup simple tool for removing duplicates from sequencing reads 20191
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0.0.2 peakcalling_ccat Control-based ChIP-seq Analysis Tool 331
ccat
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1.0.0 categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. 649
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1.0.0 cca1 Canonical Correlation Analysis 924
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1.2.0 bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. 354959
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1.0.0 blat2wig Coverage of the Reads in wiggle format 0
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1.0.0 generate_coverage_report Polymorphism of the Reads 0
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1.0.0 BestSubsetsRegression1 Perform Best-subsets Regression 298
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1.0.1 addValue Add a value as a new column. 833965
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2024.10.0+dist.h3d8a7e27 qiime2_core__tools__export qiime2_core__tools__import qiime2_core__tools__import_fastq Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 287244
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2024.10.0+q2galaxy.2024.10.0 qiime2__vsearch__cluster_features_closed_reference qiime2__vsearch__cluster_features_de_novo qiime2__vsearch__cluster_features_open_reference qiime2__vsearch__dereplicate_sequences qiime2__vsearch__fastq_stats qiime2__vsearch__merge_pairs qiime2__vsearch__uchime_denovo qiime2__vsearch__uchime_ref Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 1353
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0.0.1.dev0+q2galaxy.2024.10.0 qiime2__vizard__boxplot qiime2__vizard__heatmap qiime2__vizard__lineplot qiime2__vizard__scatterplot_2d Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 9
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2024.10.0+q2galaxy.2024.10.0 qiime2__taxa__barplot qiime2__taxa__collapse qiime2__taxa__filter_seqs qiime2__taxa__filter_table Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 7584
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0+unknown-q2galaxy.2024.10.0 qiime2__stats__alpha_group_significance qiime2__stats__collate_stats qiime2__stats__facet_across qiime2__stats__facet_within qiime2__stats__mann_whitney_u qiime2__stats__mann_whitney_u_facet qiime2__stats__plot_rainclouds qiime2__stats__prep_alpha_distribution qiime2__stats__wilcoxon_srt qiime2__stats__wilcoxon_srt_facet Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 0
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2024.10.0+q2galaxy.2024.10.0 qiime2__sample_classifier__classify_samples qiime2__sample_classifier__classify_samples_from_dist qiime2__sample_classifier__classify_samples_ncv qiime2__sample_classifier__confusion_matrix qiime2__sample_classifier__fit_classifier qiime2__sample_classifier__fit_regressor qiime2__sample_classifier__heatmap qiime2__sample_classifier__metatable qiime2__sample_classifier__predict_classification qiime2__sample_classifier__predict_regression qiime2__sample_classifier__regress_samples qiime2__sample_classifier__regress_samples_ncv qiime2__sample_classifier__scatterplot qiime2__sample_classifier__split_table qiime2__sample_classifier__summarize Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 192
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2024.10.0+q2galaxy.2024.10.0 qiime2__rescript__cull_seqs qiime2__rescript__degap_seqs qiime2__rescript__dereplicate qiime2__rescript__edit_taxonomy qiime2__rescript__evaluate_classifications qiime2__rescript__evaluate_cross_validate qiime2__rescript__evaluate_fit_classifier qiime2__rescript__evaluate_seqs qiime2__rescript__evaluate_taxonomy qiime2__rescript__extract_seq_segments qiime2__rescript__filter_seqs_length qiime2__rescript__filter_seqs_length_by_taxon qiime2__rescript__filter_taxa qiime2__rescript__get_bv_brc_genome_features qiime2__rescript__get_bv_brc_genomes qiime2__rescript__get_bv_brc_metadata qiime2__rescript__get_gtdb_data qiime2__rescript__get_ncbi_data qiime2__rescript__get_ncbi_data_protein qiime2__rescript__get_ncbi_genomes qiime2__rescript__get_silva_data qiime2__rescript__get_unite_data qiime2__rescript__merge_taxa qiime2__rescript__orient_seqs qiime2__rescript__parse_silva_taxonomy qiime2__rescript__reverse_transcribe qiime2__rescript__subsample_fasta qiime2__rescript__trim_alignment Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 21
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2024.10.0+q2galaxy.2024.10.0 qiime2__quality_filter__q_score Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 441
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2024.10.0+q2galaxy.2024.10.0 qiime2__quality_control__bowtie2_build qiime2__quality_control__decontam_identify qiime2__quality_control__decontam_identify_batches qiime2__quality_control__decontam_remove qiime2__quality_control__decontam_score_viz qiime2__quality_control__evaluate_composition qiime2__quality_control__evaluate_seqs qiime2__quality_control__evaluate_taxonomy qiime2__quality_control__exclude_seqs qiime2__quality_control__filter_reads Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 312
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2024.10.0+q2galaxy.2024.10.0 qiime2__phylogeny__align_to_tree_mafft_fasttree qiime2__phylogeny__align_to_tree_mafft_iqtree qiime2__phylogeny__align_to_tree_mafft_raxml qiime2__phylogeny__fasttree qiime2__phylogeny__filter_table qiime2__phylogeny__filter_tree qiime2__phylogeny__iqtree qiime2__phylogeny__iqtree_ultrafast_bootstrap qiime2__phylogeny__midpoint_root qiime2__phylogeny__raxml qiime2__phylogeny__raxml_rapid_bootstrap qiime2__phylogeny__robinson_foulds Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 3204
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2024.10.0+q2galaxy.2024.10.0 qiime2__metadata__distance_matrix qiime2__metadata__merge qiime2__metadata__shuffle_groups qiime2__metadata__tabulate Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 7536
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2024.10.0+q2galaxy.2024.10.0 qiime2__longitudinal__anova qiime2__longitudinal__feature_volatility qiime2__longitudinal__first_differences qiime2__longitudinal__first_distances qiime2__longitudinal__linear_mixed_effects qiime2__longitudinal__maturity_index qiime2__longitudinal__nmit qiime2__longitudinal__pairwise_differences qiime2__longitudinal__pairwise_distances qiime2__longitudinal__plot_feature_volatility qiime2__longitudinal__volatility Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 627
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2024.10.0+q2galaxy.2024.10.0 qiime2__fragment_insertion__classify_otus_experimental qiime2__fragment_insertion__filter_features qiime2__fragment_insertion__sepp Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 312
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2024.10.0+q2galaxy.2024.10.0 qiime2__feature_table__core_features qiime2__feature_table__filter_features qiime2__feature_table__filter_features_conditionally qiime2__feature_table__filter_samples qiime2__feature_table__filter_seqs qiime2__feature_table__group qiime2__feature_table__heatmap qiime2__feature_table__merge qiime2__feature_table__merge_seqs qiime2__feature_table__merge_taxa qiime2__feature_table__presence_absence qiime2__feature_table__rarefy qiime2__feature_table__relative_frequency qiime2__feature_table__rename_ids qiime2__feature_table__split qiime2__feature_table__subsample_ids qiime2__feature_table__summarize qiime2__feature_table__summarize_plus qiime2__feature_table__tabulate_feature_frequencies qiime2__feature_table__tabulate_sample_frequencies qiime2__feature_table__tabulate_seqs qiime2__feature_table__transpose Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 16881
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2024.10.0+q2galaxy.2024.10.0 qiime2__feature_classifier__blast qiime2__feature_classifier__classify_consensus_blast qiime2__feature_classifier__classify_consensus_vsearch qiime2__feature_classifier__classify_hybrid_vsearch_sklearn qiime2__feature_classifier__classify_sklearn qiime2__feature_classifier__extract_reads qiime2__feature_classifier__find_consensus_annotation qiime2__feature_classifier__fit_classifier_naive_bayes qiime2__feature_classifier__fit_classifier_sklearn qiime2__feature_classifier__makeblastdb qiime2__feature_classifier__vsearch_global Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 10050
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2024.10.0+q2galaxy.2024.10.0 qiime2__emperor__biplot qiime2__emperor__plot qiime2__emperor__procrustes_plot Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 1140
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2024.10.0+q2galaxy.2024.10.0 qiime2__diversity_lib__alpha_passthrough qiime2__diversity_lib__beta_passthrough qiime2__diversity_lib__beta_phylogenetic_meta_passthrough qiime2__diversity_lib__beta_phylogenetic_passthrough qiime2__diversity_lib__bray_curtis qiime2__diversity_lib__faith_pd qiime2__diversity_lib__jaccard qiime2__diversity_lib__observed_features qiime2__diversity_lib__pielou_evenness qiime2__diversity_lib__shannon_entropy qiime2__diversity_lib__unweighted_unifrac qiime2__diversity_lib__weighted_unifrac Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 6285
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2024.10.0+q2galaxy.2024.10.0 qiime2__diversity__adonis qiime2__diversity__alpha qiime2__diversity__alpha_correlation qiime2__diversity__alpha_group_significance qiime2__diversity__alpha_phylogenetic qiime2__diversity__alpha_rarefaction qiime2__diversity__beta qiime2__diversity__beta_correlation qiime2__diversity__beta_group_significance qiime2__diversity__beta_phylogenetic qiime2__diversity__beta_rarefaction qiime2__diversity__bioenv qiime2__diversity__core_metrics qiime2__diversity__core_metrics_phylogenetic qiime2__diversity__filter_alpha_diversity qiime2__diversity__filter_distance_matrix qiime2__diversity__mantel qiime2__diversity__partial_procrustes qiime2__diversity__pcoa qiime2__diversity__pcoa_biplot qiime2__diversity__procrustes_analysis qiime2__diversity__tsne qiime2__diversity__umap Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 11598
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2024.10.0+q2galaxy.2024.10.0 qiime2__demux__emp_paired qiime2__demux__emp_single qiime2__demux__filter_samples qiime2__demux__partition_samples_paired qiime2__demux__partition_samples_single qiime2__demux__subsample_paired qiime2__demux__subsample_single qiime2__demux__summarize qiime2__demux__tabulate_read_counts Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 6837
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2024.10.0+q2galaxy.2024.10.0 qiime2__deblur__denoise_16S qiime2__deblur__denoise_other qiime2__deblur__visualize_stats Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 1011
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2024.10.0+q2galaxy.2024.10.0 qiime2__dada2__denoise_ccs qiime2__dada2__denoise_paired qiime2__dada2__denoise_pyro qiime2__dada2__denoise_single Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 7620
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2024.10.0+q2galaxy.2024.10.0 qiime2__cutadapt__demux_paired qiime2__cutadapt__demux_single qiime2__cutadapt__trim_paired qiime2__cutadapt__trim_single Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 1710
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2024.10.0+q2galaxy.2024.10.0 qiime2__composition__add_pseudocount qiime2__composition__ancom qiime2__composition__ancombc qiime2__composition__da_barplot qiime2__composition__tabulate Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 2466
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2024.10.0+q2galaxy.2024.10.0 qiime2__alignment__mafft qiime2__alignment__mafft_add qiime2__alignment__mask Microbial ecology Phylogeny Metatranscriptomics Metagenomics Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control 1728
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0.1.2.7 segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. 1137
segalign-galaxy
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0.0.7 rdeval rdeval_report rdeval is a General purpose, multithreaded read analysis and manipulation tool. 0
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0.5.0 ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. 6465
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0.3.2-alpha ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) 1545
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0.1.2.7 kegalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. 414
kegalign-full
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1.04.22 batched_lastz Galaxy wrapper for the batching Lastz runs 678
lastz
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0.2-2 ip_wsi_extract_top_view WSI Extract Top View 88
scikit-image
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0.22.0 voronoi_tessellation Compute Voronoi tesselation Imaging Software engineering Literature and language Image analysis Image annotation Visualisation Data handling 183
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0.5-2 ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool 51
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6.0 unzip Unzip file 30662
unzip
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0.2.0 ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images Image analysis 78
superdsm
superdsm
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0.1 ip_spot_detection_2d Spot detection in 2D image sequence Imaging Bioinformatics Image analysis 237
giatools
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0.2-3 ip_split_labelmap Split Labelmaps Imaging Bioinformatics Image analysis 121
scikit-image
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2.2.3 ip_split_image Split image along axes 0
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0.3-4 ip_slice_image Slice image Imaging Bioinformatics Image analysis 335
scikit-image
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1.4 ip_segmetrics Image segmentation and object detection performance measures Image analysis 30
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0.18.3 ip_scale_image Scale image Imaging Software engineering Literature and language Image analysis Image annotation Visualisation Data handling 1429
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2023.11.12 rfove Perform segmentation region-based fitting of overlapping ellipses Cell biology Biomedical science Imaging Image analysis 45
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1.26.4 repeat_channels Convert single-channel to multi-channel image Imaging Bioinformatics Image analysis 42
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0.1.1 ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates Imaging Bioinformatics Image analysis 62337
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0.1.2 ip_projective_transformation Projective transformation Imaging Bioinformatics Image analysis 152
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0.0.3-2 ip_points_association_nn Association of points in consecutive frames Imaging Bioinformatics Image analysis 138
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0.4.1 ip_points_to_label Points to label image Imaging Bioinformatics Image analysis 146
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1.8.1 plantseg Tool for cell instance aware segmentation in densely packed 3D volumetric images Plant biology Bioimaging Light microscopy Machine learning Electron microscopy Network analysis Quantification Microscope image visualisation 0
plant-seg
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0.2-2 ip_permutate_axis Permutates axes Imaging Bioinformatics Image analysis 94
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0.0.4 ip_overlay_images Overlay two images Imaging Bioinformatics Image analysis 1020
scikit-image
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0.2.0.4 orientationpy Compute image orientation 0
orientationpy
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1.12.0 morphological_operations Apply morphological operations to images 0
scipy
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0.3-2 ip_merge_neighbours_in_label Merge Neighbours in Label Image Imaging Bioinformatics Image analysis 47
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0.7-2 ip_mahotas_features Compute image features using mahotas. 108
mahotas
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0.1.0-2 ip_landmark_registration Landmark Registration Imaging Bioinformatics Image analysis 2664
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0.2-2 ip_labelimage_to_points Label Image to Points Imaging Bioinformatics Image analysis 88
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1.26.4 label_to_binary Convert label map to binary image Imaging Bioinformatics Image analysis 0
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0.1-2 imagecoordinates_flipaxis Flip coordinate axes Imaging Bioinformatics Image analysis 63710
pandas
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0.0.3-2 ip_image_registration Intensity-based Image Registration Imaging Bioinformatics Image analysis 48
scikit-image
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1.26.4 image_math Process images using arithmetic expressions 222
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5.7.1 ip_imageinfo Extracts image metadata 1691
bftools
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0.3-2 ip_detection_viz Detection Visualization Imaging Bioinformatics Image analysis 117
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0.0.3-2 ip_curve_fitting Polynomial curve fitting to data points Imaging Bioinformatics Image analysis 87
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0.0.5-2 ip_count_objects Count Objects Imaging Bioinformatics Image analysis 1427
scikit-image
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0.0.4-2 ip_coordinates_of_roi Coordinates of ROI Imaging Bioinformatics Image analysis 47725
scikit-image
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0.3-1 ip_concat_channels Concatenate images Imaging Bioinformatics Image analysis 220
scikit-image
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3.2.1 colorize_labels Colorize label map 186
networkx
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0.9 ip_color_deconvolution Color-deconvolution methods Imaging Bioinformatics Image analysis 133
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0.7.0 bf2raw Convert image to OME-Zarr 186
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0.1-2 ip_binaryimage_to_points Binary Image to Points Imaging Bioinformatics Image analysis 63
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0.5 ip_binary_to_labelimage Binary 2 label image Imaging Bioinformatics Image analysis 3039
scikit-image
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6.7.0 ip_convertimage Convert image 6130
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0.24.0 background_removal Background removal filters using scikit-image 90
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0.4.0 ip_anisotropic_diffusion Anisotropic image diffusion 93
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1.12.0 ip_filter_standard 2d simple filter 8734
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0.18.1 ip_histogram_equalization 2d histogram equalization Imaging Software engineering Literature and language Image analysis Image annotation Visualisation Data handling 3079
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0.0.1-4 ip_2d_filter_segmentation_by_features filter segmentation by rules Imaging Bioinformatics Image analysis 8109
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0.18.1 ip_2d_feature_extraction 2D feature extraction Imaging Software engineering Literature and language Image analysis Image annotation Visualisation Data handling 15949
scikit-image
scikit-image
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
0.18.1 ip_threshold Automatic thresholding Imaging Software engineering Literature and language Image analysis Image annotation Visualisation Data handling 10729
scikit-image
scikit-image
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
0.98.2 w4mjoinpn Join positive- and negative-mode W4M datasets 490
coreutils
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
0.98.19 w4mclassfilter Filter W4M data by values or metadata 12131
r-base
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
0.98.18 w4mcorcov OPLS-DA Contrasts of Univariate Results 884
r-base
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
analysis_add_analysis analysis_get_analyses analysis_load_blast analysis_load_fasta analysis_load_gff3 analysis_load_go analysis_load_interpro analysis_sync db_index db_populate_mviews entity_publish expression_add_biomaterial expression_add_expression expression_delete_biomaterials expression_get_biomaterials expression_sync_biomaterials feature_delete_orphans feature_sync organism_add_organism organism_get_organisms organism_sync phylogeny_sync Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal 0
python-tripal
To update
2.3.8 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. 675
To update
UseGalaxy.eu1
jbrowse_to_container A tool allowing to export a JBrowse dataset into a JBrowse docker container 0
python
To update
0.4.16 genenotebook_build Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io 885
genoboo
Up-to-date
UseGalaxy.eu1 UseGalaxy.fr1
analysis_add_analysis analysis_delete_analyses analysis_get_analyses export_export_fasta export_export_gbk export_export_gff3 expression_add_biomaterial expression_add_expression expression_delete_all_biomaterials expression_delete_biomaterials expression_get_biomaterials feature_delete_features feature_get_features feature_load_fasta feature_load_featureprops feature_load_gff feature_load_go load_blast load_interpro organism_add_organism organism_delete_all_organisms organism_delete_organisms organism_get_organisms phylogeny_gene_families phylogeny_gene_order phylogeny_load_tree Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado 0
python-chado
To update
askomics_integrate Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ 0
askocli
To update
create_account feat_from_gff3 create_or_update delete_features delete_organism export fetch_jbrowse iframe list_organism Access an Apollo instance from Galaxy 13862
apollo
To update
UseGalaxy.cz9 UseGalaxy.eu9 UseGalaxy.no9
0.0.2 msp_split [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data 0
To update
1.28.0 mspurity_averagefragspectra mspurity_combineannotations mspurity_createdatabase mspurity_createmsp mspurity_dimspredictpuritysingle mspurity_filterfragspectra mspurity_flagremove mspurity_frag4feature mspurity_puritya mspurity_purityx mspurity_spectralmatching [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data 34920
bioconductor-mspurity
To update
UseGalaxy.cz10 UseGalaxy.eu10 UseGalaxy.fr11 UseGalaxy.no10
2.4.5+galaxy3 metfrag [Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity) 1770
metfrag
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
2.4.5+galaxy0 metfrag_vis [Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag 156
metfrag
To update
UseGalaxy.cz1 UseGalaxy.eu1
33 cfmid Competitive Fragmentation Modeling (CFM) 0
cfm
Up-to-date
4.0.0 abims_xcms_fillPeaks abims_xcms_group abims_xcms_refine abims_xcms_retcor abims_xcms_summary abims_xcms_xcmsSet msnbase_readmsdata xcms_export_samplemetadata xcms_merge xcms_plot_chromatogram xcms_plot_eic xcms_plot_raw Biological imaging Data visualisation Metabolomics Mass spectrum visualisation Label-free quantification Validation Filtering Chromatographic alignment Peak detection Chromatogram visualisation 8169189
bioconductor-xcms
To update
UseGalaxy.be6 UseGalaxy.cz10 UseGalaxy.eu12 UseGalaxy.fr12 UseGalaxy.no9 UseGalaxy.or11
1.0.0+galaxy1 W4Mconcatenate [W4M][Utils] concatenate two Metadata tables 12
r-base
To update
UseGalaxy.fr1
1.0.0 skyline2isocor Converting skyline output to IsoCor input 345
skyline2isocor
Up-to-date
UseGalaxy.eu1 UseGalaxy.fr1
1.0.1 physiofit_data_manager Handling of physiofit input files 27
physiofit_data_manager
Up-to-date
UseGalaxy.fr1
3.4.0 physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes 84
physiofit
Up-to-date
UseGalaxy.fr1
1.0.7+galaxy2 normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data 10254
r-batch
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
NMR_Preprocessing NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction 8134
r-batch
To update
UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
2.0.0+galaxy2 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra 171
r-batch
To update
UseGalaxy.fr1
3.0.0+galaxy1 NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation 1249
libgfortran
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
1.0.0+galaxy1 mzxmlshaper Convert mzML, mzXML or netCDF files to mzML or mzXML 1506
r-base
To update
UseGalaxy.fr1
2.2.1 ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. 471
r-base
To update
UseGalaxy.fr1
3.1.0+galaxy1 mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model 915
r-lme4
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
1.0.0 kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file 0
click
To update
1.3.1 isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments 411
jinja2
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
ipo
1.10.0 ipo4retgroup ipo4xcmsSet [W4M][LC-MS] IPO 0
bioconductor-ipo
To update
7.0.1 influx_si metabolic flux estimation based on [in]stationary labeling 54
influx_si
To update
UseGalaxy.fr1
1.0.2 influx_data_manager Handling influx_si data inputs in Galaxy workflows 27
influx-si-data-manager
To update
UseGalaxy.fr1
genform genform: generation of molecular formulas by high-resolution MS and MS/MS data 168
genform
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
0.2.1 gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs 0
To update
1.0.1+galaxy2 correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis 693
r-batch
To update
UseGalaxy.fr1
1.48.0 abims_CAMERA_annotateDiffreport abims_CAMERA_combinexsAnnos CAMERA_findAdducts CAMERA_findIsotopes CAMERA_groupCorr CAMERA_groupFWHM 49031
r-snow
To update
UseGalaxy.be1 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr6 UseGalaxy.no2 UseGalaxy.or2
0.2.5+galaxy1 wade identify regions of interest 0
wade
To update
1.1.0 tree_relabel Relabels the tips of a newick formatted tree. 0
perl-bioperl
To update
UseGalaxy.fr1
1.1.0 stringmlst Rapid and accurate identification of the sequence type (ST) 0
stringMLST
To update
UseGalaxy.fr1
0.11.0 staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Microbiology Public health and epidemiology Infectious disease Antimicrobial resistance prediction 152867
staramr
Up-to-date
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
0.3.7 srst2 Short Read Sequence Typing for Bacterial Pathogens 1161
srst2
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
1.0.1 spolpred A program for predicting the spoligotype from raw sequence reads 0
spolpred
To update
0.3.3 spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. 0
spatyper
Up-to-date
1.1.2+galaxy1 spades_header_fixer Fixes Spades Fasta ids 0
sed
To update
0.7.6 smalt SMALT aligns DNA sequencing reads with a reference genome. 0
smalt
Up-to-date
UseGalaxy.fr1
1.1.3 sistr_cmd SISTR in silico serotyping tool Whole genome sequencing Immunoproteins and antigens Sequence assembly Zoology Public health and epidemiology Genome assembly Visualisation Multilocus sequence typing 14537
sistr_cmd
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
1.0.1 seqtk_nml_sample Tool to downsample fastq reads 0
seqtk
To update
0.1.2 refseq_masher_contains refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. 16983
refseq_masher
Up-to-date
UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
0.7.0 aacoverage aavariants callcodonvar callntvar complexity_bam complexity_fasta consensus distance dnds drmutations hydra quality A collection of tools for analysing Viral Quasispecies 42837
quasitools
Up-to-date
UseGalaxy.fr12 UseGalaxy.or12
1.0.0 pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. 0
perl-bioperl
To update
1.2 promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them 0
python
To update
1.2.1 pneumocat Pneumococcal Capsular Typing of illumina fastq reads 0
pneumocat
Up-to-date
1.1 plasmidspades Genome assembler for assemblying plasmid 0
spades
To update
UseGalaxy.fr1
Plasmid Profiler suite defining all dependencies for Plasmid Profiler 0
To update
0.1.6 plasmid_profiler Explores plasmid content in WGS data 0
r
To update
UseGalaxy.fr1
0.1.2 patrist Extract Patristic Distance From a Tree 0
python
To update
1.1.14 pangolin Phylogenetic Assignment of Named Global Outbreak LINeages 59046
pangolin
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
0.1.4.1 mykrobe_parseR RScript to parse the results of mykrobe predictor. 0
r-base
To update
1.0.2 mrbayes A program for the Bayesian estimation of phylogeny. 0
mrbayes
To update
UseGalaxy.be1 UseGalaxy.fr1
3.1.9 mob_recon mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies Metagenomics Sequence assembly Genotype and phenotype Mobile genetic elements Genomics Clustering Sequence analysis 580707
mob_suite
Up-to-date
UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
1.0.10 mauve_contig_mover Order a draft genome relative to a related reference genome 0
mauve
To update
2.3 kat_@EXECUTABLE@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. 0
kat
To update
2.3 kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes 0
kat
To update
0.3.0 kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. 0
kaptive
To update
1.0.1 hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. 0
hivtrace
To update
1.1.0 gnali A tool to find nonessential, loss-of-function gene variants 0
gnali
Up-to-date
0.1.4.1 getmlst Download MLST datasets by species from pubmlst.org 0
srst2
To update
UseGalaxy.fr1
1.0.1 filter_spades_repeat Remove short and repeat contigs/scaffolds 0
perl-bioperl
To update
UseGalaxy.fr1
0.1.0 feht Automatically identify makers predictive of groups. 0
feht
To update
1.2 FastQC_Summary Summary multiple FastQC into a single tabular line report 0
perl-bioperl
To update
1.1.0 fa-extract-sequence extract single fasta from multiple fasta file 4281
perl-bioperl
To update
UseGalaxy.fr1
1.0.0 fasta2bed Convert multiple fasta file into tabular bed file format 0
perl-bioperl
To update
2.0.0 ectyper EC-Typer - in silico serotyping of Escherichia coli species Whole genome sequencing Public health and epidemiology Sequence assembly Genotype and phenotype Workflows Sequence assembly Read pre-processing Variant calling 49737
ectyper
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
0.20.0 csvtk_awklike_filter csvtk_awklike_mutate csvtk_collapse csvtk_concat csvtk_convert csvtk_correlation csvtk_cut csvtk_filter csvtk_freq csvtk_gather csvtk_join csvtk_mutate csvtk_plot csvtk_replace csvtk_sample csvtk_separate csvtk_sort csvtk_split csvtk_summary csvtk_uniq Rapid data investigation and manipulation of csv/tsv files 372
csvtk
To update
UseGalaxy.fr20 UseGalaxy.or6
1.0 CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. 35706
cryptogenotyper
Up-to-date
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
0.2 concat_fastqs Concatenate paired datasets 0
To update
0.1 combine Combine Tabular Collection into a single file 0
To update
1.0 combine_stats Combine multiple Assemblystats datasets into a single tabular report 0
perl-getopt-long
To update
0.1 combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. 0
To update
5.1.0 collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection 285258
gawk
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
1.3.0 bundle_collection Tool to bundle up list collection into a single zip to be download 10704
perl-getopt-long
To update
UseGalaxy.fr1 UseGalaxy.or1
0.2.0 bionumeric_convert Convert BioHansel output data to a Bionumerics friendly form 0
pandas
To update
2.4.0 biohansel Heidelberg and Enteritidis SNP Elucidation 0
bio_hansel
To update
1.0.0 bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. 0
bamclipper
Up-to-date
UseGalaxy.fr1
1.1.0 bam2mappingstats Generates mapping stats from a bam file. 0
perl
To update
1.1.0 assemblystats Summarise an assembly (e.g. N50 metrics) 0
perl-bioperl
To update
UseGalaxy.fr1
1.1 abacas Order and Orientate Contigs 0
mummer
To update
UseGalaxy.fr1
13.45.0.4846264 t_coffee T-Coffee 16626
t-coffee
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
1.0 smina Scoring and Minimization with smina 1647
smina
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
0.1.0 smart_domains SMART domains 0
perl-bioperl
To update
0.1 replace_chromosome_names Replace chromosome names 1559
python
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
1.0 rdock Docking ligands to proteins and nucleic acids 0
rDock
To update
1.0 plotheatmap Plot heatmap of gene expression data 0
bioconductor-preprocesscore
To update
UseGalaxy.fr1
3.3a+galaxy1 miranda Finds potential target sites for miRNAs in genomic sequences 20535
miranda
To update
UseGalaxy.eu1 UseGalaxy.fr1
2.32 lotus2 LotuS2 OTU processing pipeline Metagenomics Taxonomy Microbial ecology Sequence feature detection DNA barcoding 5241
lotus2
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
0.3.0 hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids 781
python
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
0.5.1.1 hcluster_sg Hierarchically clustering on a sparse graph 779
hcluster_sg
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
0.4.3 gstf_preparation GeneSeqToFamily preparation converts data for the workflow 977
python
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
0.91b gblocks Gblocks 1740
gblocks
Up-to-date
UseGalaxy.be1 UseGalaxy.fr1 UseGalaxy.or1
0.1.0 export_to_cluster Export datasets to cluster 0
python
To update
ete
3.1.3 ete_gene_csv_finder ete_genetree_splitter ete_homology_classifier ete_init_taxdb ete_lineage_generator ete3_mod ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit Phylogenetics Phylogenetic analysis Phylogenetic tree editing 2351
ete
ete3
To update
UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.fr7 UseGalaxy.no7
0.2.0 blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input 1599
python
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
1.0+galaxy1 apoc Large-scale structural comparison of protein pockets 27
apoc
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
1.9.2.post0 treebest_best TreeBeST best Phylogenetics Phylogenetic tree visualisation Phylogenetic analysis Phylogenetic inference (from molecular sequences) 3013
treebest
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
0.4.1 gafa Gene Align and Family Aggregator 107
python
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
1.0.0 get_feature_info get_genetree get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. 3761
python
To update
UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.no3
2.1 peptimapper_clustqualify peptimapper_clust_to_gff peptimapper_pep_match peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes 18
To update
UseGalaxy.fr4
0.1.0 openlabcds2csv Creates a summary of several "Internal Standard Report" OpenLabCDS results. 0
openjdk
To update
0.2 miranda2asko Converts miRanda output into AskOmics format 0
perl
To update
1.5.2 meneco Meneco computes minimal completions to your draft network with reactions from a repair network 0
meneco
Up-to-date
1.7.8 logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence 0
logol
Up-to-date
0.3.3 helixer Gene calling with Deep Neural Networks Sequence analysis Gene transcripts Gene prediction Genome annotation 3039
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
0.3 get_pairs Separate paired and unpaired reads from two fastq files 0
python
To update
0.1.0 gcms2isocor Conversion from GCMS PostRun Analysis to Isocor 0
openjdk
To update
0.1 feelnc2asko Convert FeelNC GTF to GFF3 0
perl-bioperl
To update
3.0.8 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . RNA-Seq Genomics Structure prediction Sequence analysis Genome annotation Gene prediction 11784
To update
UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
2.1.6 braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . 651
To update
UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1
1.1.0 baric_archive_rennes baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. 48
To update
UseGalaxy.fr2
0.2 askor_de AskoR links EdgeR and AskOmics 9
bioconductor-limma
To update