Workflows

FastQC39 MultiQC27 SAMtools23 anndata22 ggplot216 SCANPY15 Bowtie 214 Cutadapt14 fastp14 BWA13 scikit-learn13 Bandage12 JBrowse12 BEDTools11 BUSCO11 Minimap211 mothur11 QUAST11 BamTools9 BCFtools9 DeepTools9 FreeBayes9 kraken29 NanoPlot8 seqtk8 Trim Galore8 BLAST7 Galaxy Image Analysis7 MaxQuant7 msConvert7 STAR7 taxonomy_krona_chart7 Trimmomatic7 DESeq26 GEMINI6 gffread6 HISAT26 MACS6 MuSiC Deconvolution6 Open Babel6 scikit-image6 DropletUtils5 FeatureCounts5 Flye5 RSeQC5 SRA Software Toolkit5 StringTie5 Unicycler5 annotatemyids4 Biopython4 bx-python4 Galactic Circos4 gffcompare4 GOseq4 KrakenTools4 MAFFT4 MEGAHIT4 Racon4 Salmon4 Stacks4 Unipept4 UniProt4 Bracken3 Bwa-mem23 Cardinal3 Clustal 2 (Clustal W, Clustal X)3 COMBAT-TB Workbench3 Falco3 GenomeScope 2.03 Gromacs3 HUMAnN23 InterProScan (EBI)3 Merqury3 MetaPhlAn3 MSstats3 MSstatsTMT3 Newick Utilities3 Prokka3 pyGenomeTracks3 R3 snippy3 UMI-tools3 Vcflib3 Bakta2 bed to protein map2 Bio3D2 CellProfiler2 ChEMBL2 chemfp2 compute_sequence_length2 cshl_fastx_reverse_complement2 customProDB2 Diamond2 EGA2 eggNOG-mapper v22 epiScanpy2 FastTree2 FASTX-Toolkit2 funannotate2 gfastats2 GOEnrichment2 humann2 limma2 lofreq2 MAKER2 MDAnalysis2 Medaka2 MEME2 MetaNovo2 metaQuantome2 metaspades2 miniasm2 NCBI Resources2 NGSUtils2 The Protein Data Bank (PDB)2 QIIME2 RDKit2 Recentrifuge2 RepeatMasker2 sceasy2 SeqCode2 Seurat2 SnapATAC2 snpEff2 staramr2 tb-profiler2 tbl2gff32 Workflow4Metabolomics2 xcms2 ABRicate1 AmberTools1 antiSMASH1 Apollo1 AUGUSTUS1 blockbuster1 Bowtie1 BRAKER31 ChemicalToolbox1 ChIPpeakAnno1 ChiRA1 Circos1 Clair31 clusterProfiler1 CNVkit1 dada21 diaPASEF1 edgeR1 EGSEA1 European Nucleotide Archive (ENA)1 ete1 ewastools1 export2graphlan1 FEELnc1 fgsea1 Filtlong1 FlashLFQ1 FREEC1 GAEVAL1 GECKO1 g:Profiler1 GraPhlAn1 Heinz1 Helixer1 HiCExplorer1 The Immune Epitope Database (IEDB)1 Integron Finder1 iqtree1 ISEScan1 IsoformSwitchAnalyzeR1 IWTomics1 kraken-biom1 Krona1 LASTZ1 lotus21 MAGeCK1 MALDIquant1 Matchms1 MethylDackel1 MFAssignR1 miRDeep21 multiGSEA1 mzToSQLite1 OBITools1 OMArk1 OptiType1 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 Seq2HLA1 shovill1 sinto1 Smudgeplots1 SNAP1 SortMeRNA1 SPAdes1 SuCOS1 Targetfinder.org1 TransDecoder1 TRANSIT1 trimAl1 Trinity1 Trinotate1 VarScan1 varVAMP1 VelvetOptimiser1 WoLF PSORT1 More...

Galaxy350

GTN339 Galaxy338 Transcriptomics32 Proteomics27 Ecology21 genome-annotation16 variant-analysis16 microbiome15 Statistics14 Assembly12 epigenetics11 Computational-chemistry10 Name:clinicalmp10 single-cell10 Introduction9 Lg-wf9 Ml9 name:single-cell9 name:training9 Galaxy-interface8 imaging8 Name:singlecell8 Name:transcriptomics8 Name:neoantigen7 Climate6 Metabolomics6 Name:microgalaxy6 Sequence-analysis6 evolution5 name:Collection5 Name:iwc5 Name:pathogfair5 Earth-system4 Metagenomics4 Name:deconv-eval4 Name:scrna-seq4 Ocean4 BY-COVID3 Cheminformatics3 covid-193 hCNV3 Name:by-covid3 Name:trajectory_analysis3 pangeo3 synthetic-biology3 Visualisation3 CellProfiler2 Classification2 Contributing2 Ecoregionalization2 FAIR workflows2 GC-MS2 Marineomics2 Microgalaxy2 MIRACUM2 Name:seurat2 scATAC-seq2 Segmentation2 vgp2 10X1 Alternative splicing1 alternative-splicing1 Arabidopsis1 Asaim1 Beacon1 Big-data1 bioimaging1 Braker31 BUSCO1 cancer1 Chinese-language1 Chowell_train_test1 Clustering1 CNVkit1 Comparison1 copernicus1 Cut&run1 Deeplearning1 Diff1 Digitalhumanities1 Exposomics1 Expospomics1 Fnn1 Formulaassignment1 Fungi1 Genomeannotation1 Genomics1 Geosciences1 hla1 Humanities1 IDR1 Iedb1 imageanaylsis1 Imagerecognition1 Introductions1 isoform switching1 Iwtomics1 Jbrowse1 Llr6_model1 Logistic_regression_model1 Loris1 Lotus21 Ludwig1 Metaplasmidome1 Mirna1 Mito-flash1 Mitochondrion_tracking1 Mnist1 Moleculardynamics1 Multi-omics1 Name:bacsnp1 Name:baculoviridae1 Name:baculovirus1 Name:circos1 Name:data-management1 Name:deconvolution1 name:ERGA1 Name:gtn1 Name:naldv1 Name:nanopore1 Name:sequenceanalysis1 Name:single_cell1 Name:viz1 Noiseestimation1 pathogen1 Pseudobulk1 Published1 Pubmed1 Pubtator1 QCxMS1 Recalibration1 referencegenome1 Regression1 Reviewed1 rna1 Sempi31 Smfish1 synthetic data1 Text1 Text_mining1 Text-mining1 tuberculosis1 VGP_curated1 visualization1 Voronoi1 workflow1 More...

GTN Bot337 Helena Rasche4 Cristóbal Gallardo3 Khaled Jum'ah2 Pauline Seguineau2 Bert Droesbeke1 Saskia Hiltemann1 More...

Galaxy Training Network350 BY-COVID (general)2

Galaxy350 ELIXIR2

Cristóbal Gallardo3 Pauline Seguineau2 Krzysztof Poterlowicz1 Willem de Koning1 Anne Fouilloux1 Helena Rasche1 Jasper Ouwerkerk1 Saskia Hiltemann1 Khaled Jum'ah1 More...

BY-COVID related workflows2

Copy number variation2 Ecology2 Transcriptomics2 Biomedical science1 Data visualisation1 Genetic variation1 Microbiology1 More...

Copy number variation detection2 Antimicrobial resistance prediction1 Copy number estimation1 Genetic mapping1 Sequencing quality control1 Structural variation detection1 Transcriptome assembly1 Visualisation1 More...

Stable8 Work-in-progress3