From e6df2689d3be6d5a64c81d062d6bb6f76cbf7773 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Tue, 9 Jul 2024 16:19:12 +0200 Subject: [PATCH] Add index pages --- results/assembly/index.html | 59 + results/biodiversity/index.html | 59 + results/imaging/index.html | 59 + results/index.html | 59 + results/machine-learning/index.html | 59 + results/microgalaxy/index.html | 59 + results/spoc/index.html | 7122 +-------------------------- 7 files changed, 413 insertions(+), 7063 deletions(-) create mode 100644 results/assembly/index.html create mode 100644 results/biodiversity/index.html create mode 100644 results/imaging/index.html create mode 100644 results/index.html create mode 100644 results/machine-learning/index.html create mode 100644 results/microgalaxy/index.html diff --git a/results/assembly/index.html b/results/assembly/index.html new file mode 100644 index 00000000..a9feda5e --- /dev/null +++ b/results/assembly/index.html @@ -0,0 +1,59 @@ + + + + + + Simple HTML Page + + + +
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Assembly ressources from the Galaxy Codex

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Biodiversity ressources from the Galaxy Codex

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+ + diff --git a/results/imaging/index.html b/results/imaging/index.html new file mode 100644 index 00000000..92568084 --- /dev/null +++ b/results/imaging/index.html @@ -0,0 +1,59 @@ + + + + + + Simple HTML Page + + + +
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Imaging ressources from the Galaxy Codex

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Galaxy ressources from the Galaxy Codex

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Machine-learning ressources from the Galaxy Codex

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microGalaxy ressources from the Galaxy Codex

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+ + diff --git a/results/spoc/index.html b/results/spoc/index.html index e65fd810..4eb38539 100644 --- a/results/spoc/index.html +++ b/results/spoc/index.html @@ -1,7063 +1,59 @@ - - - - - - - - - - - - - - - - - - - - -
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ExpandGalaxy wrapper idGalaxy tool idsDescriptionbio.tool idbio.tool idsbiiibio.tool namebio.tool descriptionEDAM operationEDAM topicStatusSourceToolShed categoriesToolShed idGalaxy wrapper ownerGalaxy wrapper sourceGalaxy wrapper parsed folderGalaxy wrapper versionConda idConda versionEDAM operation (no superclasses)EDAM topic (no superclasses)Available on UseGalaxy.org (Main)Available on UseGalaxy.org.auAvailable on UseGalaxy.euAvailable on UseGalaxy.frTools available on UseGalaxy.org (Main)Tools available on UseGalaxy.org.auTools available on UseGalaxy.euTools available on UseGalaxy.frTools available on ANASTASIATools available on APOSTLTools available on ARGs-OAPTools available on BF2I-MAPTools available on BioBixTools available on CIRM-CFBPTools available on Center for Phage Technology (CPT)Tools available on ChemFlowTools available on Coloc-statsTools available on CorGATTools available on CropGalaxyTools available on DintorTools available on FreeBioinfoTools available on GASLINITools available on Galaxy@AuBiTools available on Galaxy@PasteurTools available on GalaxyTrakrTools available on Genomic HyperbrowserTools available on GigaGalaxyTools available on HyPhy HIV NGS ToolsTools available on IPK Galaxy Blast SuiteTools available on ImmPort GalaxyTools available on InteractoMIXTools available on MISSISSIPPITools available on Mandoiu LabTools available on MiModD NacreousMapTools available on OqtansTools available on PalfinderTools available on PepSimiliTools available on PhagePromotorTools available on ProtologgerTools available on UseGalaxy.beTools available on UseGalaxy.czTools available on UseGalaxy.noNo. of tool users (2022-2023) (usegalaxy.eu)Total tool usage (usegalaxy.eu)Deprecated
aegeanaegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parsevalAEGeAn toolkit wrappersgaevalgaevalGAEVALGene Annotation EVAluation.Sequence annotationSequence analysis, Gene structureUp-to-datehttps://github.com/BrendelGroup/AEGeAnTranscriptomics, Sequence Analysisaegeaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/aegeanhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean0.16.0aegean0.16.0Sequence annotationSequence analysis, Gene structure14441444000000000000000000000000000000004047168
anndataanndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loomImport, Export, Inspect and Manipulate Anndata and Loom objectsTo updatehttps://anndata.readthedocs.ioTranscriptomics, Sequence Analysisanndataiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata0.10.3anndata0.6.22.post154505450000000000000000000000000000000005562535620
arribaarriba, arriba_draw_fusions, arriba_get_filtersArriba detects fusion genes in RNA-Seq data after running RNA-STARUp-to-datehttps://github.com/suhrig/arribaSequence Analysis, Transcriptomicsarribaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/arribahttps://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba2.4.0arriba2.4.0033003300000000000000000000000000000000030383528
askoraskor_deAskoR links EdgeR and AskOmicsTo updatehttps://github.com/askomics/askoRTranscriptomicsaskor_degenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/askorhttps://github.com/genouest/galaxy-tools/tree/master/tools/askor0.2bioconductor-limma3.58.100000000000000000000000000000000000000000000
bamparsebamparseGenerates hit count lists from bam alignments.To updatehttp://artbio.frRNA, Transcriptomicsbamparseartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/bamparsehttps://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse4.1.1pysam0.22.100000000000000000000000000000001000000000000
baredscbaredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2dbaredSC 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.baredscbaredscbaredSCThe baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) 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.Data retrieval, Expression correlation analysis, Differential gene expression profilingRNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probabilityUp-to-datehttps://github.com/lldelisle/baredSCTranscriptomics, Visualizationbaredsciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/baredschttps://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc1.1.3baredsc1.1.3Data retrieval, Expression correlation analysis, Differential gene expression profilingRNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability404040400000000000000000000000000000000040071
bctoolsbctools_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_eventsbctools 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 2.0Up-to-datehttps://github.com/dmaticzka/bctoolsSequence Analysis, Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtoolshttps://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools0.2.2bctools0.2.2007000700000000000000000000000000000000077872895
brew3r_rbrew3r_rExtend 3' end of a GTF using another GTF as a templateTo updatehttps://bioconductor.org/packages/release/bioc/html/BREW3R.r.htmlTranscriptomics, RNAbrew3r_riuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_rhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r1.0.210001000000000000000000000000000000000000000
cell-types-analysisct_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_pvalsTools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysisTo updateTranscriptomics, RNA, Statisticssuite_cell_types_analysisebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis1.1.1cell-types-analysis0.1.1100600060000000000000000000000000000000000026
cemitoolcemitoolGene co-expression network analysis toolcemitoolcemitoolCEMiToolIt unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.Enrichment analysis, Pathway or network analysisGene expression, Transcriptomics, Microarray experimentTo updatehttps://www.bioconductor.org/packages/release/bioc/html/CEMiTool.htmlTranscriptomics, RNA, Statisticscemitooliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitoolhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool1.18.1bioconductor-cemitool1.26.0Enrichment analysis, Pathway or network analysisTranscriptomics, Microarray experiment101010100000000000000000000000000000000010998
cherricherri_eval, cherri_trainComputational Help Evaluating RNA-RNA interactionscherricherricherriCheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.Molecular interactions, pathways and networks, Structure analysis, Machine learningTo updatehttps://github.com/BackofenLab/CherriTranscriptomics, RNAiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cherrihttps://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri0.7cherri0.8Molecular interactions, pathways and networks, Structure analysis, Machine learning0020002000000000000000000000000000000000201207
chirachira_collapse, chira_extract, chira_map, chira_merge, chira_quantifyChimeric Read Annotator for RNA-RNA interactome datachirachiraChiRAChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNAUp-to-datehttps://github.com/pavanvidem/chiraRNA, Transcriptomics, Sequence Analysischiraiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/chirahttps://github.com/galaxyproject/tools-iuc/tree/main/tools/chira1.4.3chira1.4.3Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA505050500000000000000000000000000000000055976418
cite_seq_countcite_seq_countCount CMO/HTOCITE-seq-CountCITE-seq-CountCITE-seq-CountTool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.RNA-Seq quantificationTranscriptomics, Immunoproteins and antigensUp-to-datehttps://github.com/Hoohm/CITE-seq-CountTranscriptomicscite_seq_countiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_counthttps://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count1.4.4cite-seq-count1.4.4RNA-Seq quantificationTranscriptomics, Immunoproteins and antigens101010100000000000000000000000000000000010118
cosgcosgMarker gene identification for single-cell sequencing data using COSG.Up-to-datehttps://github.com/genecell/COSGTranscriptomics, Sequence Analysiscosgiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg1.0.1cosg1.0.100000000000000000000000000000000000000000000
cpatcpatCoding-potential assessment tool using an alignment-free logistic regression model.Up-to-datehttps://github.com/liguowang/cpatTranscriptomicscpatbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/cpathttps://github.com/bgruening/galaxytools/tree/master/tools/cpat3.0.5cpat3.0.511111111000000000000000000000000000000001021134
cpm_tpm_rpkcpm_tpm_rpkGenerate CPM,TPM or RPK from raw countsTo updatehttp://artbio.frTranscriptomicscpm_tpm_rpkartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpkhttps://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk0.5.2r-optparse1.3.200000000000000000000000010000001000000000000
crosscontamination_barcode_filtercrosscontamination_barcode_filterBarcode contamination discovery toolTo updateTranscriptomics, Visualizationcrosscontamination_barcode_filteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filterhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter0.3r-ggplot22.2.110101010000000000000000000000000000000001117347
cuffcomparecuffcompareGalaxy wrappers for the Cuffcompare tool.Up-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffcomparedevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcomparehttps://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare2.2.1cufflinks2.2.1111111110000001000000001000000010010000011651130
cuffdiffcuffdiffGalaxy wrappers for the Cuffdiff tool.Up-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffdiffdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiffhttps://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff2.2.1cufflinks2.2.11010101000010010000000010000000000100000112285831
cufflinkscufflinksGalaxy wrappers for the Cufflinks tool.Up-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscufflinksdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinkshttps://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks2.2.1cufflinks2.2.111111111000000100000000110010001001000001131932218
cuffmergecuffmergeGalaxy wrappers for the Cuffmerge tool.Up-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffmergedevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmergehttps://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge2.2.1cufflinks2.2.11111111100000010000000000000000100100000111223292
cuffnormcuffnormThe Cuffnorm toolUp-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffnormdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnormhttps://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm2.2.1cufflinks2.2.111101110000000000000000000000001000000001127660
cuffquantcuffquantThe Cuffquant toolUp-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffquantdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquanthttps://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant2.2.1cufflinks2.2.111101110000000000000000000000001000000001118688
data-hcahca_matrix_downloaderTools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projectsTo updateTranscriptomics, Sequence Analysissuite_human_cell_atlas_toolsebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hcav0.0.4+galaxy0hca-matrix-downloader0.0.400100010000000000000000000000000000000001134439
data-scxaretrieve_scxaTools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/homeTo updateTranscriptomics, Sequence Analysissuite_ebi_expression_atlasebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxav0.0.2+galaxy2wget11111111000000000000000000000000000000001199799
decouplerscore_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulkdecoupler - Ensemble of methods to infer biological activitiesTo updatehttps://decoupler-py.readthedocs.io/en/latest/Transcriptomicssuite_decouplerebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler1.4.0+galaxy3decoupler1.5.000100010000000000000000000000000000000000006
deg_annotatedeg_annotateAnnotate DESeq2/DEXSeq output tablesTo updateTranscriptomicsdeg_annotateiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotatehttps://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate1.1.0bedtools2.31.1111111110000000000000010100100000000000011177419910
deseq2deseq2Differential gene expression analysis based on the negative binomial distributionDESeq2DESeq2DESeq2R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.Differential gene expression analysis, RNA-Seq analysisRNA-SeqTo updatehttps://www.bioconductor.org/packages/release/bioc/html/DESeq2.htmlTranscriptomics, RNA, Statisticsdeseq2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq22.11.40.8bioconductor-deseq21.42.0Differential gene expression analysis, RNA-Seq analysisRNA-Seq111111110001001000000011100100010000010011499095752
deseq2_normalizationdeseq2_normalizationNormalizes gene hitlistsTo updatehttp://artbio.frRNA, Transcriptomics, Sequence Analysis, Statisticsdeseq2_normalizationartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalizationhttps://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization1.40.2+galaxy0bioconductor-deseq21.42.000000000000000000000000000010001000000000000
dexseqdexseq, dexseq_count, plotdexseqInference of differential exon usage in RNA-SeqdexseqdexseqDEXSeqThe package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.Enrichment analysis, Exonic splicing enhancer predictionRNA-SeqUp-to-datehttps://www.bioconductor.org/packages/release/bioc/html/DEXSeq.htmlTranscriptomics, RNA, Statisticsdexseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseqhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq1.48.0bioconductor-dexseq1.48.0Enrichment analysis, Exonic splicing enhancer predictionRNA-Seq33333333000000000000000000000000000000003321816064
dropletutilsdropletutils_empty_drops, dropletutils_read_10xDe-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_dropletutilsebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils1.0.4dropletutils-scripts0.0.52020202000000000000000000000000000000000202011599
dropletutilsdropletutilsDropletUtils - Utilities for handling droplet-based single-cell RNA-seq datadropletutilsdropletutilsDropletUtilsProvides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.Loading, Community profilingGene expression, RNA-seq, Sequencing, TranscriptomicsTo updatehttps://bioconductor.org/packages/devel/bioc/html/DropletUtils.htmlTranscriptomics, Sequence Analysisdropletutilsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils1.10.0bioconductor-dropletutils1.22.0Sequencing, Transcriptomics1111111100000000000000000001000000000000111263934
edgeredgerPerform RNA-Seq differential expression analysis using edgeR pipelineedgeredgeredgeRDifferential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.Differential gene expression analysisGenetics, RNA-Seq, ChIP-seqTo updatehttp://bioconductor.org/packages/release/bioc/html/edgeR.htmlTranscriptomics, RNA, Statisticsedgeriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/edgerhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/edger3.36.0bioconductor-edger4.0.16Differential gene expression analysisGenetics, RNA-Seq, ChIP-seq11111111000000100000001010010001000000001194518117
egseaegseaThis tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testingegseaegseaEGSEAThis package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.Gene set testingSystems biologyTo updatehttps://bioconductor.org/packages/release/bioc/html/EGSEA.htmlTranscriptomics, RNA, Statisticsegseaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/egseahttps://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea1.20.0bioconductor-egsea1.28.0Gene set testingSystems biology1110111000000000000000000000000000000000111772524
fastq_providerfastq_providerRetrieval and download of FASTQ files from ENA and other repositories such as HCA.To updatehttps://github.com/ebi-gene-expression-group/atlas-fastq-providerData Source, RNA, Transcriptomicsatlas_fastq_providerebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_providerhttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider0.4.4atlas-fastq-provider0.4.700000000000000000000000000000000000000000000
fastq_utilsfastq_filter_n, fastq_trim_poly_atSet of tools for handling fastq filesTo updatehttps://github.com/nunofonseca/fastq_utilsTranscriptomics, RNAfastq_utilsebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utilshttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils0.25.1+galaxy0fastq_utils0.25.200000000000000000000000000000000000000000000
featurecountsfeaturecountsfeatureCounts counts the number of reads aligned to defined masked regions in a reference genomefeaturecountsfeaturecountsFeatureCountsfeatureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.Read summarisation, RNA-Seq quantificationRNA-SeqTo updatehttp://bioinf.wehi.edu.au/featureCountsRNA, Transcriptomics, Sequence Analysisfeaturecountsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecountshttps://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts2.0.3subread2.0.6Read summarisation, RNA-Seq quantificationRNA-Seq1111111100000010000000111001000100000100114679696399
fgseafgseaPerform gene set testing using fgseafgseafgseafgseaThe package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.Gene-set enrichment analysisGeneticsTo updatehttps://bioconductor.org/packages/release/bioc/html/fgsea.htmlVisualization, Transcriptomics, Statisticsfgseaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fgseahttps://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea1.8.0+galaxy1bioconductor-fgsea1.28.0Gene-set enrichment analysisGenetics1111111100000000000000000000000000000000113075240
garnettgarnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_fileDe-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_garnettebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett0.2.8garnett-cli0.0.5007000700000000000000000000000000000000000327
genomic_super_signaturegenomic_super_signatureInterpretation of RNAseq experiments through robust, efficient comparison to public databasesgenomicsupersignaturegenomicsupersignatureGenomicSuperSignatureGenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reductionRNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experimentTo updatehttps://github.com/shbrief/GenomicSuperSignatureSequence Analysis, RNA, Transcriptomicsgenomic_super_signatureiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signaturehttps://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature1.2.0bioconductor-genomicsupersignature1.10.0Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reductionRNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment0010001000000000000000000000000000000000101146
gffcomparegffcompareGalaxy wrappers for Geo Pertea's GffCompare package.gffcomparegffcomparegffcompareProgram for comparing, annotating, merging and tracking transcripts in GFF files.Sequence annotationNucleic acids, Sequence analysisUp-to-datehttps://github.com/gpertea/gffcompare/Transcriptomicsgffcompareiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcomparehttps://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare0.12.6gffcompare0.12.6Sequence annotationNucleic acids, Sequence analysis1111111100000000000000100000000000000000113813477
gsc_filter_cellsfilter_cellsFilter single cell RNAseq data on libray depth and number of detected genesTo updatehttp://artbio.frTranscriptomicsgsc_filter_cellsartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cellshttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells4.3.1+galaxy0r-optparse1.3.200000000000000000000000000000000000000000000
gsc_filter_genesfilter_genesFilter genes that are detected in less than a fraction of libraries in single cell RNAseq dataTo updatehttp://artbio.frTranscriptomicsgsc_filter_genesartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_geneshttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes4.3.1+galaxy0r-optparse1.3.200000000000000000000000000000000000000000000
gsc_gene_expression_correlationssingle_cell_gene_expression_correlationsCompute single-cell paire-wise gene expressions correlationsTo updatehttp://artbio.frTranscriptomicsgsc_gene_expression_correlationsartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlationshttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations4.3.1+galaxy0r-optparse1.3.200000000000000000000000000000000000000000000
gsc_high_dimensions_visualisationhigh_dimensions_visualisationGenerates PCA, t-SNE and HCPC visualisationTo updatehttp://artbio.frTranscriptomics, Visualizationgsc_high_dimensions_visualisationartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualizationhttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation4.3+galaxy0r-optparse1.3.200000000000000000000000000000000000000000000
gsc_mannwhitney_demannwhitney_dePerform a mann-whitney differential testing between two sets of gene expression dataTo updatehttp://artbio.frTranscriptomicsgsc_mannwhitney_deartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_dehttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de4.1.3+galaxy0r-optparse1.3.200000000000000000000000000000000000000000000
gsc_scran_normalizescran_normalizeNormalize raw counts using scranTo updatehttp://artbio.frTranscriptomicsgsc_scran_normalizeartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalizehttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize1.28.1+galaxy0bioconductor-scran1.30.00010001000000000000000000000000000000000101478
gsc_signature_scoresignature_scoreCompute signature scores from single cell RNAseq dataTo updatehttp://artbio.frTranscriptomicsgsc_signature_scoreartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_scorehttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score2.3.9+galaxy0r-optparse1.3.200000000000000000000000000000000000000000000
heinzheinz_bum, heinz, heinz_scoring, heinz_visualizationAn algorithm for identification of the optimal scoring subnetwork.heinzheinz, bionetHeinzTool for single-species active module discovery.Pathway or network analysisGenetics, Gene expression, Molecular interactions, pathways and networksTo updatehttps://github.com/ls-cwi/heinzTranscriptomics, Visualization, Statisticsheinziuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/heinzhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz1.0bioconductor-bionet1.62.0Pathway or network analysisGenetics, Gene expression, Molecular interactions, pathways and networks4440444000000000000000000000000000000000442421186
isoformswitchanalyzerisoformswitchanalyzerStatistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.IsoformSwitchAnalyzeRIsoformSwitchAnalyzeRIsoformSwitchAnalyzeREnables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.Sequence comparison, Sequence analysisComputational biology, Gene transcriptsTo updatehttps://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.htmlTranscriptomics, RNA, Statisticsisoformswitchanalyzeriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzerhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer1.20.0bioconductor-isoformswitchanalyzer2.2.0Sequence comparison, Sequence analysisComputational biology, Gene transcripts11111111000000000000000000000000000000001029822
kallistokallisto_pseudo, kallisto_quantkallisto 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.kallistokallistokallistoA program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.Gene expression profilingTranscriptomics, RNA-seq, Gene expressionTo updatehttps://pachterlab.github.io/kallisto/Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto0.48.0kallisto0.50.1Gene expression profilingTranscriptomics22222222000000000000000220000000000000002229924155
limma_voomlimma_voomPerform RNA-Seq differential expression analysis using limma voom pipelinelimmalimmalimmaData analysis, linear models and differential expression for microarray data.RNA-Seq analysisMolecular biology, GeneticsUp-to-datehttp://bioconductor.org/packages/release/bioc/html/limma.htmlTranscriptomics, RNA, Statisticslimma_voomiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voomhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom3.58.1bioconductor-limma3.58.1RNA-Seq analysisMolecular biology, Genetics111111110000000000000000000000000000000011101220344
masigpromasigproIdentify significantly differential expression profiles in time-course microarray experimentsmasigpromasigpromaSigProRegression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.Regression analysisGene expression, Molecular genetics, Microarray experiment, RNA-SeqTo updatehttps://www.bioconductor.org/packages/release/bioc/html/maSigPro.htmlTranscriptomics, RNA, Statisticsmasigproiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/masigprohttps://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro1.49.3coreutils8.25Regression analysisGene expression, Microarray experiment, RNA-Seq10101010000000000000000000000000000000001113576
mircountsmircountsGenerates miRNA count lists from read alignments to mirBase.To updatehttp://artbio.frRNA, Transcriptomicsmircountsartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/mircountshttps://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts1.6tar01000100000000000000000000000001000000000000
monocle3monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkersDe-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_monocle3ebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle30.1.4monocle3-cli0.0.99090909000000000000000000000000000000000002643266
multigseamultigseaGSEA-based pathway enrichment analysis for multi-omics datamultiGSEAmultiGSEAmultiGSEAA GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.Gene-set enrichment analysis, Aggregation, Pathway analysisMetabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small moleculesUp-to-datehttps://bioconductor.org/packages/devel/bioc/html/multiGSEA.htmlTranscriptomics, Proteomics, Statisticsmultigseaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/multigseahttps://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea1.12.0bioconductor-multigsea1.12.0Gene-set enrichment analysis, Aggregation, Pathway analysisMetabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules001000100000000000000000000000000000000010253
music_deconvolutionmusic_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolutionMulti-subject Single Cell deconvolution (MuSiC)Up-to-datehttps://github.com/xuranw/MuSiCTranscriptomicsmusicbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/music/https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution0.1.1music-deconvolution0.1.15540554000000000000000000000000000000000502401872
nugen_nudupnugen_nudupMarks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.nudupnudupNuDupMarks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.Duplication detectionSequencingUp-to-datehttps://github.com/tecangenomics/nudupSAM, Metagenomics, Sequence Analysis, Transcriptomicsnugen_nudupiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nuduphttps://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup2.3.3nudup2.3.3Duplication detectionSequencing00000000000000000000000000000000000000000000
pathifierpathifierpathifierUp-to-datehttps://Transcriptomics, Statisticspathifierartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/pathifierhttps://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier1.40.0bioconductor-pathifier1.40.000100010000000000000000000000000000000001010228
pizzlypizzlyPizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.To updatehttps://github.com/pmelsted/pizzly/Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly0.37.3.1pizzly0.37.310101010000000000000000000000000000000001116208
psiclasspsiclassPsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.psiclasspsiclassUp-to-datehttps://github.com/splicebox/PsiCLASSTranscriptomicspsiclassiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclasshttps://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass1.0.3psiclass1.0.3001000100000000000000000000000000000000010115
qualimapqualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseqqualimapqualimapQualiMapPlatform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.Sequencing quality controlData quality managementTo updatehttp://qualimap.bioinfo.cipf.es/Sequence Analysis, Transcriptomics, SAMqualimapiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimaphttps://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap2.2.2dqualimap2.3Sequencing quality controlData quality management4441444100000000000000004001000100000000441328664470
raceidraceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectoryRaceID3, StemID2, FateID - scRNA analysisTo updatehttps://github.com/dgrun/RaceID3_StemID2_package/Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid0.2.3r-raceid0.1.3555155510000000000000000000000000000000055824569
repenrichedger-repenrich, repenrichRepeat element profilingTo updatehttps://github.com/ARTbio/tools-artbio/tree/main/tools/repenrichTranscriptomicsrepenrichartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/repenrichhttps://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2.31.102000200000000000000000000000002000000000000
repenrich2edger-repenrich2, repenrich2Repeat element profiling using bowtie2 alignerTo updatehttps://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2Transcriptomicsrepenrich2artbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich22.31.100000000000000000000000000000002000000000000
rgrnastarrna_star, rna_starsoloRNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapperstarstarSTARUltrafast universal RNA-seq data alignerSequence alignmentRNA-Seq, TranscriptomicsTo updatehttps://github.com/alexdobin/STARNext Gen Mappers, Transcriptomicsrgrnastariuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastarhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar2.7.11astar2.7.11bSequence alignmentRNA-Seq, Transcriptomics2222222200010000000000111002000100000100224015425658
ribowaltzribowaltz_process, ribowaltz_plotCalculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling datariboWaltzriboWaltzriboWaltzriboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.Computational biologyTo updatehttps://github.com/LabTranslationalArchitectomics/riboWaltzTranscriptomics, RNAiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltzhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz1.2.0ribowaltz2.0Computational biology00200020000000000000000000000000000000002014161
rsemextract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtietranscript quantification from RNA-Seq dataTo updatehttps://github.com/deweylab/RSEMTranscriptomics, RNArsemartbiohttps://github.com/artbio/tools-artbio/tree/master/tools/rsemhttps://github.com/ARTbio/tools-artbio/tree/main/tools/rsemrsem1.3.300100010000000000000000000000004000000001167377
rseqcrseqc_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_tinan RNA-seq quality control packagerseqcrseqcRSeQCProvides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.Data handlingSequencingUp-to-datehttps://code.google.com/p/rseqc/Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualizationrseqcnileshhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc5.0.3rseqc5.0.3Data handlingSequencing2222222222222222000000000000000000022000220000000022223206133498
ruvseqruvseqRemove Unwanted Variation from RNA-Seq DataruvseqruvseqRUVSeqThis package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.Differential gene expression analysisGene expression, RNA-seqTo updatehttps://www.bioconductor.org/packages/release/bioc/html/DESeq2.htmlTranscriptomics, RNA, Statisticsruvseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseqhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq1.26.0bioconductor-ruvseq1.36.0Differential gene expression analysisGene expression101010100000000000000000000000010000000011761236
salmonalevin, salmon, salmonquantmergeSalmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.salmonsalmonSalmonA tool for transcript expression quantification from RNA-seq dataSequence composition calculation, RNA-Seq quantification, Gene expression analysisRNA-Seq, Gene expression, TranscriptomicsTo updatehttps://github.com/COMBINE-lab/salmonSequence Analysis, RNA, Transcriptomicsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/salmonhttps://github.com/bgruening/galaxytools/tree/master/tools/salmon1.10.1salmon1.10.3Sequence composition calculation, RNA-Seq quantification, Gene expression analysisRNA-Seq, Transcriptomics21312131000000000000000210010001000000003396961937
sashimi_plotsashimi_plotGenerates a sashimi plot from bam files.To updatehttp://artbio.frRNA, Transcriptomics, Graphics, Visualizationsashimi_plotartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plothttps://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot0.1.1python00000000000000000000000010000000000000000000
sc3sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepareDe-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_sc3ebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc31.8.0sc3-scripts0.0.600700070000000000000000000000000000000000019
scanpyscanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confoundersScanpy – Single-Cell Analysis in PythonscanpyscanpySCANPYScalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.Differential gene expression analysisGene expression, Cell biology, GeneticsTo updatehttps://scanpy.readthedocs.ioTranscriptomics, Sequence Analysisscanpyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy1.9.6scanpy1.7.2Differential gene expression analysisGene expression, Cell biology, Genetics66606660000000000000000000000000000000006676651978
scanpyanndata_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_datascanpy-scripts, command-line wrapper scripts around Scanpy.To updatehttps://scanpy.readthedocs.ioTranscriptomics, Sequence Analysis, RNAscanpy_scriptsebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpyhttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy1.9.3scanpy-scripts1.9.30122272702227270000000000000000000000000000000001413218539356
scaterscater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_resultsDe-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_scaterebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater1.10.0scater-scripts0.0.501600160000000000000000000000000000000002216387
scaterscater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsneScater (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.scaterscaterscaterPre-processing, quality control, normalization and visualization of single-cell RNA-seq data.Read pre-processing, Sequencing quality control, Sequence visualisationRNA-seq, Quality affairs, Molecular geneticsTo updatehttp://bioconductor.org/packages/scater/Transcriptomics, RNA, Visualizationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scaterhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/scater1.22.0bioconductor-scater1.30.1Read pre-processing, Sequence visualisationQuality affairs, Molecular genetics055005500000000000000000000000000000000055771365
sccafrun_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_outSCCAF: Single Cell Clustering Assessment Framework.To updatehttps://github.com/sccaf/sccafTranscriptomicsSCCAFebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccafhttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf0.0.9sccaf0.0.100040004000000000000000000000000000000000002110
sceasysceasy_convertConverter between difference single-cell formatsUp-to-datehttps://github.com/cellgeni/sceasy/Transcriptomicssceasy_convertiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy0.0.7r-sceasy0.0.710101010000000000000000000000001000000000090721
sceasysceasy_convertConvert scRNA data object between popular formatsTo updateTranscriptomicssceasyebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy0.0.5r-sceasy0.0.710101010000000000000000000000001000000000090721
schicexplorerschicexplorer_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_schicqualitycontrolscHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.To updatehttps://github.com/joachimwolff/schicexplorerSequence Analysis, Transcriptomics, Visualizationschicexploreriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorerhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer4schicexplorer7001600016000000000000000000000000000000000161623779
scmapscmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_featuresDe-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_scmapebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap1.6.4scmap-cli0.1.00070007000000000000000000000000000000000101383
scpipescpipeA flexible preprocessing pipeline for single-cell RNA-sequencing datascpipescpipescPipeA preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.Genome annotation, Validation, Alignment, VisualisationGene expression, RNA-Seq, SequencingTo updatehttp://bioconductor.org/packages/release/bioc/html/scPipe.htmlTranscriptomics, RNA, Statisticsscpipeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipehttps://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe1.0.0+galaxy2bioconductor-scpipe2.2.0Genome annotation, Validation, Alignment, VisualisationGene expression, RNA-Seq10101010000000000000000000000000000000001111628
scpredscpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_modelDe-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_scpredebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred1.0.2scpred-cli0.1.0004000400000000000000000000000000000000000425
seuratseuratA toolkit for quality control, analysis, and exploration of single cell RNA sequencing dataTo updatehttps://github.com/satijalab/seuratTranscriptomics, RNA, Statisticsseuratiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seurathttps://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat4.3.0.1r-seurat3.0.2111111110000000000000000000000010000000011661543
seuratseurat_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_featuresDe-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1Up-to-datehttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/Transcriptomics, RNA, Statistics, Sequence Analysissuite_seuratebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat4.0.0seurat-scripts4.0.0001411001411000000000000000000000001900000000001811966
slamdunkalleyoop, slamdunkSlamdunk maps and quantifies SLAMseq readsUp-to-datehttp://t-neumann.github.io/slamdunkRNA, Transcriptomics, Sequence Analysis, Next Gen Mappersslamdunkiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunkhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk0.4.3slamdunk0.4.32020202000000000000000000000000000000000222361
sleuthsleuthSleuth is a program for differential analysis of RNA-Seq data.sleuthsleuthsleuthA statistical model and software application for RNA-seq differential expression analysis.Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculationRNA-seq, Gene expression, Statistics and probabilityUp-to-datehttps://github.com/pachterlab/sleuthTranscriptomics, RNA, Statisticssleuthiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuthhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth0.30.1r-sleuth0.30.1Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculationGene expression, Statistics and probability001000100000000000000000000000000000000010864
star_fusionstar_fusionSTAR Fusion detects fusion genes in RNA-Seq data after running RNA-STARTo updateSequence Analysis, Transcriptomicsstar_fusioniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusionhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion0.5.4-3+galaxy1star-fusion1.13.0111011100000000000000010000000000000000011351212
stringtiestringtie, stringtie_mergeStringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.stringtiestringtieStringTieFast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.Transcriptome assembly, RNA-Seq analysisTranscriptomics, RNA-seqUp-to-datehttp://ccb.jhu.edu/software/stringtie/Transcriptomicsstringtieiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtiehttps://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie2.2.3stringtie2.2.3Transcriptome assembly, RNA-Seq analysisTranscriptomics2222222200000000000000200000000000000200222165167659
tophat_fusion_posttophat_fusion_postWrapper for Tophat-Fusion post stepTo updateTranscriptomicstophat_fusion_postdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_posthttps://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post0.1blast+01100110000000000000000000000000000000001115216
transdecodertransdecoderTransDecoder finds coding regions within transcriptsTransDecoderTransDecoderTransDecoderTransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.Coding region prediction, de Novo sequencing, De-novo assemblyGenomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencingTo updatehttps://transdecoder.github.io/Transcriptomics, RNAtransdecoderiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoderhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder5.5.0transdecoder5.7.1Coding region prediction, de Novo sequencing, De-novo assemblyGenomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing1111111100000000000010001000000000000000113485468
trinitytrinity_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_statsTrinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseqtrinitytrinityTrinityTrinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.Transcriptome assemblyTranscriptomics, Gene expression, Gene transcriptsUp-to-datehttps://github.com/trinityrnaseq/trinityrnaseqTranscriptomics, RNAiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/trinityhttps://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity2.15.1trinity2.15.1Transcriptome assemblyTranscriptomics, Gene transcripts913131391313130000000000000012100000011001000001312176231951
trinotatetrinotateTrinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.trinotatetrinotateTrinotateComprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.Gene functional annotationGene expression, TranscriptomicsTo updatehttps://trinotate.github.io/Transcriptomics, RNAtrinotateiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotatehttps://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate3.2.2trinotate4.0.2Gene functional annotationTranscriptomics1110111000000000000000001000000000000000111511796
tximporttximportWrapper for the Bioconductor package tximporttximporttximporttximportAn R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.Pathway or network analysis, Formatting, RNA-Seq analysisTranscriptomics, Gene transcripts, WorkflowsTo updatehttp://bioconductor.org/packages/tximport/Transcriptomicstximportiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tximporthttps://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport1.22.0bioconductor-tximport1.30.0Pathway or network analysis, Formatting, RNA-Seq analysisTranscriptomics, Gene transcripts, Workflows101010100000000000000000000000000000000011881408
ucsc-cell-browserucsc_cell_browserPython pipeline and Javascript scatter plot library for single-cell datasetsTo updatehttps://cells.ucsc.edu/Transcriptomicsucsc_cell_browserebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.ymlhttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser1.0.0+galaxy1ucsc-cell-browser1.2.600100010000000000000000000000000000000001178941
umi_toolsumi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelistUMI-tools extract - Extract UMIs from fastqumi-toolsumi-toolsUMI-toolsTools for handling Unique Molecular Identifiers in NGS data sets.Sequencing quality controlNGS, Sequence sites, features and motifs, Quality affairsTo updatehttps://github.com/CGATOxford/UMI-toolsSequence Analysis, Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_toolshttps://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools1.1.2umi_tools1.1.5Sequencing quality controlSequence sites, features and motifs, Quality affairs55555555000000000000000010000005000000005537961618
velocytovelocyto_cliVelocyto is a library for the analysis of RNA velocity.Up-to-datehttp://velocyto.org/Transcriptomicsvelocytoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/velocytohttps://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto0.17.17velocyto.py0.17.1710101010000000000000000000000000000000001002
volcanoplotvolcanoplotTool to create a Volcano PlotTo updatehttps://ggplot2.tidyverse.org/Visualization, Transcriptomics, Statisticsvolcanoplotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplothttps://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot0.0.6r-ggplot22.2.1111111110000000000000010100000010000000011174930946
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