Workflows

FastQC41 MultiQC30 SAMtools23 anndata22 ggplot216 Bowtie 215 Cutadapt15 fastp15 SCANPY15 BEDTools13 BWA13 JBrowse13 scikit-learn13 Bandage12 BUSCO12 Minimap211 mothur11 QUAST11 FreeBayes10 taxonomy_krona_chart10 BamTools9 BCFtools9 DeepTools9 kraken29 Trimmomatic9 BLAST8 Galaxy Image Analysis8 msConvert8 NanoPlot8 scikit-image8 seqtk8 STAR8 Trim Galore8 gffread7 HISAT27 MaxQuant7 DESeq26 GEMINI6 MACS6 MuSiC Deconvolution6 Open Babel6 StringTie6 Biopython5 bx-python5 DropletUtils5 FASTX-Toolkit5 FeatureCounts5 Flye5 gffcompare5 RSeQC5 SRA Software Toolkit5 Unicycler5 annotatemyids4 Falco4 Galactic Circos4 GOseq4 KrakenTools4 MAFFT4 MEGAHIT4 MetaPhlAn4 pyGenomeTracks4 Racon4 Salmon4 Stacks4 Unipept4 UniProt4 bed to protein map3 Bracken3 Bwa-mem23 Cardinal3 Clustal 2 (Clustal W, Clustal X)3 COMBAT-TB Workbench3 customProDB3 GenomeScope 2.03 Gromacs3 humann3 InterProScan (EBI)3 Merqury3 MSstats3 MSstatsTMT3 Newick Utilities3 Prokka3 R3 snippy3 UMI-tools3 Vcflib3 Bakta2 Bio3D2 biomformat2 BRAKER32 CellProfiler2 ChEMBL2 chemfp2 compute_sequence_length2 cshl_fastx_reverse_complement2 Diamond2 EGA2 eggNOG-mapper v22 epiScanpy2 export2graphlan2 FastTree2 funannotate2 gfastats2 GOEnrichment2 GraPhlAn2 Helixer2 HiCExplorer2 HUMAnN22 The Immune Epitope Database (IEDB)2 limma2 lofreq2 MAKER2 MAPseq2 MDAnalysis2 Medaka2 MEME2 MetaNovo2 metaQuantome2 metaspades2 miniasm2 NCBI Resources2 NGSUtils2 OMArk2 OptiType2 The Protein Data Bank (PDB)2 PRINSEQ2 QIIME2 RDKit2 Recentrifuge2 RepeatMasker2 sceasy2 Seq2HLA2 SeqCode2 Seurat2 SnapATAC2 snpEff2 SortMeRNA2 staramr2 tb-profiler2 tbl2gff32 Workflow4Metabolomics2 xcms2 ABRicate1 AmberTools1 ampvis1 antiSMASH1 Apollo1 AUGUSTUS1 blockbuster1 Bowtie1 ChemicalToolbox1 ChIPpeakAnno1 ChiRA1 Circos1 Clair31 clusterProfiler1 cmsearch-deoverlap1 CNVkit1 Combine Metaphlan and HUMAnN1 CoverM1 dada21 diaPASEF1 edgeR1 EGSEA1 European Nucleotide Archive (ENA)1 ete1 ewastools1 FEELnc1 fgsea1 Filtlong1 FlashLFQ1 FREEC1 GAEVAL1 GECKO1 g:Profiler1 Heinz1 Infernal1 Integron Finder1 iqtree1 ISEScan1 IsoformSwitchAnalyzeR1 IWTomics1 kraken-biom1 Krona1 LASTZ1 lotus21 MAGeCK1 MALDIquant1 Matchms1 MethylDackel1 MFAssignR1 miRDeep21 multiGSEA1 mzToSQLite1 OBITools1 pangolin1 pathview1 Peakachu1 PfamScan1 phyloseq1 pilon1 PlasFlow1 PlasmidFinder1 Polypolish1 Prodigal1 Proteinortho1 PubMed1 purge_dups1 PyTorch1 QualiMap1 QuickTree1 RaceID1 RAMClustR1 RapidNJ1 RAxML1 RCAS1 RED1 RIAssigner1 rnaQUAST1 SALSA1 scater1 shovill1 sinto1 Smudgeplots1 SNAP1 SPAdes1 SuCOS1 Targetfinder.org1 TransDecoder1 TRANSIT1 trimAl1 Trinity1 Trinotate1 VarScan1 varVAMP1 VelvetOptimiser1 WoLF PSORT1 More...

Galaxy372

GTN361 Galaxy360 Transcriptomics32 Proteomics27 Ecology22 microbiome21 genome-annotation16 variant-analysis16 Name:neoantigen14 Statistics14 Assembly12 epigenetics12 Name:microgalaxy12 Computational-chemistry10 Metagenomics10 Name:clinicalmp10 single-cell10 Introduction9 Lg-wf9 Ml9 name:single-cell9 name:training9 Galaxy-interface8 imaging8 Name:singlecell8 Name:transcriptomics8 Amplicon6 Climate6 Metabolomics6 Mgnify_amplicon6 Sequence-analysis6 evolution5 name:Collection5 Name:iwc5 Name:pathogfair5 Earth-system4 Flexynesis4 Machine_learning4 Name:deconv-eval4 Name:scrna-seq4 Ocean4 BY-COVID3 Cheminformatics3 covid-193 hCNV3 Name:by-covid3 Name:trajectory_analysis3 pangeo3 synthetic-biology3 Visualisation3 Braker32 BUSCO2 CellProfiler2 Classification2 Contributing2 Ecoregionalization2 FAIR workflows2 GC-MS2 Genomeannotation2 hla2 Iedb2 Jbrowse2 Marineomics2 Microgalaxy2 MIRACUM2 Name:seurat2 scATAC-seq2 Segmentation2 vgp2 10X1 Alternative splicing1 alternative-splicing1 annotation pipeline1 Asaim1 Augustus1 Beacon1 Big-data1 Biodiversity1 Bioimage1 bioimaging1 cancer1 Chinese-language1 Chowell_train_test1 Clustering1 CNVkit1 Comparison1 copernicus1 Cut&run1 Deep_learning1 Deeplearning1 Diff1 Digitalhumanities1 Electrophoresis_gel1 Environmental monitoring1 eukaryotic genome1 Exposomics1 Expospomics1 Fnn1 Formulaassignment1 Fungi1 gene prediction1 GeneMark-ET1 Genomics1 Geosciences1 Habitat fragmentation1 Helixer1 Humanities1 IDR1 imageanaylsis1 Imagerecognition1 Introductions1 isoform switching1 Iwtomics1 Land cover classification1 Landscape ecology1 Llr6_model1 Logistic_regression_model1 Loris1 Lotus21 Ludwig1 Metaplasmidome1 Mito-flash1 Mitochondrion_tracking1 Mnist1 Moleculardynamics1 Multi-omics1 Name:bacsnp1 Name:baculoviridae1 Name:baculovirus1 Name:band_intensity1 Name:bioimaging1 Name:circos1 Name:data-management1 Name:deconvolution1 name:ERGA1 Name:gtn1 Name:naldv1 Name:nanopore1 Name:qupath1 Name:sequenceanalysis1 Name:single_cell1 Name:viz1 Noiseestimation1 pathogen1 Plant1 protein evidence1 Pseudobulk1 Published1 Pubmed1 Pubtator1 QCxMS1 Recalibration1 referencegenome1 Regression1 Reviewed1 rna1 rna-seq1 Roi1 Sempi31 Sentinel-21 Smfish1 synthetic data1 Tabpfn1 Text1 Text_mining1 Text-mining1 training1 tuberculosis1 Vegetation1 Vegetation index1 VGP_curated1 visualization1 Voronoi1 workflow1 yolo1 More...

GTN Bot359 Helena Rasche4 Cristóbal Gallardo3 Khaled Jum'ah2 Pauline Seguineau2 Bert Droesbeke1 Saskia Hiltemann1 More...

Galaxy Training Network372 EuroScienceGateway18 BY-COVID (general)2

Galaxy372 ELIXIR20

Marie Jossé8 Anthony Bretaudeau6 Yvan Le Bras3 Cristóbal Gallardo3 Romane Libouban3 Helena Rasche2 Pauline Seguineau2 Krzysztof Poterlowicz1 Willem de Koning1 Anne Fouilloux1 Alexandre Cormier1 Laura Leroi1 Jasper Ouwerkerk1 Saskia Hiltemann1 Khaled Jum'ah1 Eli Chadwick1 Patrick Austin1 More...

BY-COVID related workflows2 Biodiversity & ecology workflows1

Ecology3 Copy number variation2 Transcriptomics2 Biodiversity1 Biomedical science1 Data visualisation1 Genetic variation1 Microbiology1 More...

Copy number variation detection2 Antimicrobial resistance prediction1 Copy number estimation1 Gene prediction1 Genetic mapping1 Genome annotation1 Read mapping1 Sequence alignment1 Sequence assembly1 Sequencing quality control1 Structural variation detection1 Transcriptome assembly1 Visualisation1 More...

Stable24 Work-in-progress3