Workflows

MultiQC67 FastQC58 SAMtools55 fastp47 BUSCO35 BWA34 Minimap231 anndata27 Bowtie 227 Cutadapt26 BEDTools24 SCANPY24 ggplot222 Bandage21 kraken220 BLAST19 QUAST19 BCFtools18 gfastats17 Merqury16 taxonomy_krona_chart15 JBrowse14 seqtk14 SRA Software Toolkit14 MACS13 scikit-learn13 Bwa-mem212 GenomeScope 2.012 gffread12 NanoPlot12 STAR12 Trimmomatic12 BamTools11 FreeBayes11 mothur11 StringTie11 DeepTools10 Flye10 Open Babel10 DESeq29 HISAT29 lofreq9 MaxQuant9 Stacks9 Trim Galore9 UniProt9 Galaxy Image Analysis8 msConvert8 R8 Unicycler8 Biopython7 bx-python7 FASTX-Toolkit7 Galaxy7 MaBoSS7 MAFFT7 PhysiCell7 purge_dups7 Racon7 RSeQC7 scikit-image7 shovill7 snpEff7 GEMINI6 Gromacs6 KrakenTools6 MuSiC Deconvolution6 QualiMap6 RDKit6 RepeatMasker6 Seurat6 TransDecoder6 Vcflib6 antiSMASH5 Bracken5 compleasm5 DropletUtils5 FeatureCounts5 GOseq5 iqtree5 Konstanz Information Miner (KNIME)5 Medaka5 MEGAHIT5 Scipion5 seqkit5 SPAdes5 Unipept5 annotatemyids4 CellProfiler4 Clustal 2 (Clustal W, Clustal X)4 COMBAT-TB Workbench4 Cufflinks4 Diamond4 funannotate4 Galactic Circos4 gffcompare4 InterProScan (EBI)4 MSstats4 Newick Utilities4 NGSUtils4 PretextView4 Salmon4 Smudgeplots4 snippy4 Workflow4Metabolomics4 xcms4 ABRicate3 AmberTools3 Bakta3 Cardinal3 ChiRA3 cisTEM3 compute_sequence_length3 eggNOG-mapper v23 Falco3 FastTree3 HiCExplorer3 HUMAnN23 Infernal3 MAKER3 MAPseq3 Meryl3 MetaNovo3 MetaPhlAn3 metaspades3 MotionCor23 MSstatsTMT3 Nextflow3 OMArk3 picard_samtofastq3 Prokka3 pyGenomeTracks3 Recentrifuge3 SeqCode3 staramr3 tb-profiler3 ToolDistillator3 UMI-tools3 VarScan3 Variant Effect Predictor (VEP)3 YaHS3 AutoDock2 AutoDock Vina2 BBMap2 bed to protein map2 Bio3D2 BioContainers2 biomformat2 BRAKER12 cBioPortal2 CheckM2 ChEMBL2 chemfp2 ChemicalToolbox2 Clair32 clusterProfiler2 CNVkit2 cshl_fastx_reverse_complement2 customProDB2 edgeR2 EGA2 epiScanpy2 FEELnc2 Filtlong2 GATK2 GOEnrichment2 Helixer2 Hifiasm2 humann2 Integron Finder2 ISEScan2 iVar2 limma2 Matchms2 MaxBin2 MDAnalysis2 MEME2 MetaBAT 22 metaQuantome2 MFAssignR2 miniasm2 nanopolish2 NCBI Datasets2 NCBI Resources2 OBITools2 P2Rank2 The Protein Data Bank (PDB)2 Picard2 pilon2 PlasmidFinder2 PredPrIn2 PRINSEQ2 Prodigal2 Proteinortho2 QIIME2 RepeatModeler2 sceasy2 Scipion-chem2 SemiBin2 Snakemake2 SnapATAC2 SnpSift2 SuCOS2 tbl2gff32 tophat22 VADR2 vardict2 vcfanno2 vcfutils2 VSEARCH2 XMIPP2 AdapterRemoval1 AGAT1 ampvis1 AnnotSV1 Apollo1 AUGUSTUS1 AutoSite1 Binette1 Bioconductor1 BlobToolKit1 blockbuster1 Bowtie1 BRAKER31 CARNIVAL1 ChIPpeakAnno1 Circos1 Clustal 1.8 (Clustal W, Clustal X)1 cmsearch-deoverlap1 CONCOCT1 CoverM1 cuffdiff1 dada21 dastool1 decoupleR1 DeepVariant1 Delly21 diaPASEF1 dRep1 EGSEA1 EMBOSS1 European Nucleotide Archive (ENA)1 ete1 ewastools1 export2graphlan1 FGENESH1 fgsea1 FLASH1 FlashLFQ1 Foldseek1 Fpocket1 FREEC1 GADES1 GAEVAL1 gblocks1 GBMatch - GBMPredictor1 GECKO1 GetOrganelle1 ggtree1 g:Profiler1 GraPhlAn1 GSEA1 GTDB-Tk1 hAMRonization1 Heinz1 HiFiAdapterFilt1 htseqcount1 HTSlib1 The Immune Epitope Database (IEDB)1 ImageJ21 IsoformSwitchAnalyzeR1 IWTomics1 JBrowse 21 kraken-biom1 Krona1 LASTZ1 lotus21 MAGeCK1 MALDIquant1 Mash1 MethylDackel1 miniprot1 miRDeep21 MitoHiFi1 MITOS1 MOB-suite1 MolMeDB1 Metagenomic operational taxonomic units (mOTUs)1 MSMetaEnhancer1 multiGSEA1 MUMmer1 mzToSQLite1 ngsReports1 OptiType1 pangolin1 pathview1 Peakachu1 PEAR1 PfamScan1 phyloseq1 PhysiBoSS1 PlasFlow1 PLINK1 Polypolish1 progeny1 protexcluder1 PubMed1 pyfastaq1 PyTorch1 qcxms1 QuickTree1 RaceID1 RAMClustR1 RapidNJ1 RAxML1 RCAS1 recetox-msfinder1 RED1 RepeatModeler1 RIAssigner1 rnaQUAST1 SALSA1 scater1 Seq2HLA1 SeqSero21 sinto1 SISTR1 SNAP1 snipit1 SortMeRNA1 Subread1 tabix1 Targetfinder.org1 TaxonKit1 TRANSIT1 trimAl1 Trinity1 Trinotate1 TSSr1 UCSC Genome Browser Utilities1 VAPOR1 varlociraptor1 varVAMP1 VelvetOptimiser1 WGCNA1 WoLF PSORT1 xtb1 More...

Galaxy652 Nextflow147 Common Workflow Language82 COMPSs66 Python48 Snakemake46 Jupyter35 Docker17 Shell Script14 KNIME13 Playbook Workflow Builder Workflow9 Workflow Description Language8 R markdown7 Scipion7 Bpipe5 Argo Workflow2 Autosubmit2 BioCompute Object1 DVC1 Janis1 Perl1 Pi1 Plug-in1 Quarto Markdown1 Rbbt1 Uniform Interface to Computing Resources1 More...

Galaxy354 GTN340 Bioinformatics70 Genomics53 Transcriptomics51 PyCOMPSs47 covid-1946 Assembly44 Proteomics40 Supercomputer37 Metagenomics35 data_persistence32 Ecology25 Workflows25 genome-annotation23 Nextflow23 imaging22 Marenostrum IV22 non_data_persistence22 Annotation21 CWL20 microbiome20 rna19 Alignment18 Python18 rna-seq18 COMPSs17 SNPs17 dislib16 single-cell16 Statistics16 variant-analysis16 workflow16 ERGA15 INDELs15 Machine Learning15 variant calling14 cancer13 GATK413 nanopore13 RNASEQ13 epigenetics12 Example12 illumina12 image processing12 Marenostrum V12 name:single-cell12 Tutorial12 variant_calling12 Climate11 Metabolomics11 name:training11 Cheminformatics10 Computational-chemistry10 HiFi10 Name:clinicalmp10 ONT10 QC10 FASTQ9 Introduction9 Large-genome-assembly9 Lg-wf9 Ml9 SARS-CoV-29 vgp9 Earth-system8 FAIR workflows8 Galaxy-interface8 Laptop8 Name:singlecell8 Name:transcriptomics8 scRNAseq8 Snakemake8 softwareRequirements8 WGS8 bioimaging7 Java7 Name:neoantigen7 Ocean7 scalable7 TSI-annotation7 variant-calling7 astronomy6 Classification6 DNA6 evolution6 Genome assembly6 genome_assembly6 Hi-C6 mass-spectrometry6 molecular dynamics6 name:Collection6 Name:microgalaxy6 PBS6 Sequence-analysis6 Virology6 Virus6 antimicrobial resistance5 bacterial-genomics5 bpipe5 BY-COVID5 ChIP5 ChIP-seq5 copernicus5 covid19.galaxyproject.org5 genome5 groovy5 jupyter5 Knime5 mapping5 Name:iwc5 Name:pathogfair5 NCI5 pangeo5 pediatric5 phylogenetics5 remote_dataset5 SAMTools5 scipion5 shotgun5 ABRomics4 AMR4 ARTIC4 BGE4 binning4 Biodiversity4 BUSCO4 CellProfiler4 Databases4 EOSC4Cancer4 Gadi4 generic4 Germline4 gpu4 helicase4 HPC4 Multi-omics4 name:ASSEMBLY+QC4 Name:deconv-eval4 name:ONT4 Name:scrna-seq4 NGS4 OMERO4 openms4 pathogen4 rare diseases4 RDM4 Retrosynthesis4 rna virus4 scATAC-seq4 scRNA-seq4 Segmentation4 spa4 10xgenomics3 16S3 Amplicon3 AMR-detection3 Assembly+QC3 ATAC-seq3 BWA3 BWA-mem3 Conversion3 cryoem3 DataQC3 Default-SDR3 denovo-assembly3 eDNA3 Epigenomics3 FAIR3 FastQC3 GC-MS3 genome-assembly3 hCNV3 HiC3 hifiasm3 identification3 kallisto3 kraken3 long-read-sequencing3 manta3 Merqury3 Metabarcoding3 MetaDEGalaxy3 metatranscriptomics3 MultiQC3 Name:by-covid3 name:ERGA3 name:ILLUMINA3 Name:trajectory_analysis3 NCI-Gadi3 OME-Zarr3 paired-end3 Pathway Analysis3 pathway prediction3 protein3 quality3 S33 SANBI3 Somatic3 STAR3 structural variants3 synthetic-biology3 taxonomic-classification3 taxonomic-profiling3 transcriptome3 Visualisation3 10X2 10x-genomics2 18S2 adna2 Alternative splicing2 alternative-splicing2 annotsv2 antibiotic-resistance2 antimicrobial-resistance-genes2 BAM2 bash2 BioID2 blast2 BROAD2 C++2 cage2 cage-seq2 cageseq-data2 Cellranger2 CNVkit2 CODEX22 collections2 Consensus2 Contributing2 Copy Number Variation2 coronavirus2 cosifer2 CTE-Power92 Deep learning2 demultiplexing2 dengue2 DE_NOVO2 differential-expression2 DNA-seq2 Drug design2 DT-GEO2 earth observation2 Ecoregionalization2 Electron microscopy2 ExomeDepth2 exploration2 Exposomics2 expression2 fasta2 Flashlite2 gene set enrichment analysis2 Geophysics2 Glacios2 GROMACS2 GUCFG2galaxy2 GWAS2 hla2 human2 HySEA2 image-processing2 ITS2 k-mer2 linkage_map2 long-reads2 Marineomics2 MARS-seq2 Matrix Multiplication2 MERS2 Meryl2 metabolic engineering2 metagenome2 microbial2 Microgalaxy2 MIRACUM2 mirna prediction2 mpxv2 multi-specimen-input2 name:public-data2 Name:seurat2 nanopore-sequencing2 NCI Gadi2 NSP132 pacbio2 pangenome2 pathway design2 peak-calling2 personalized medicine2 phasing2 phylogenomics2 phylogeny2 Pipeline2 Profiling2 protein-structure2 proteogenomics2 PyTorch2 QCxMS2 quality control2 quantification2 Quast2 R2 referencegenome2 Report2 Reviewed2 scientific publication text mining2 Semantic Network Analysis2 sequence annotation2 single-cell-rna-seq2 singularity2 snv2 star-solo2 structural-variants2 Supernova2 SVD2 synteny2 Synthetic Biology2 synthetic data2 TalosArctica2 taxonomy-assignment2 TitanKrios2 Tophat22 training2 TransBioNet2 trinity2 TSI2 Tsunami2 tuberculosis2 validated-2022-06-292 variation2 VARSCAN22 VCF2 Virtual Drug Screening2 visualization2 WDL2 wes2 west nile2 whole genome sequencing2 zika2 #single-cell1 10.3390/microorganisms100202921 ABR1 abricate1 adaptor1 air-quality1 airr1 alevin1 alphafold21 amp1 amplicon-sequencing1 ampliconarchitect1 ampliconsuite1 ancient-dna1 ancient-dna-analysis1 ancientdna1 antimicrobial-peptides1 Arabidopsis1 arg1 Asaim1 atac1 ATACseq1 AutoDock1 automated workflows1 b-cell1 BackTrackBB1 bacteria1 bacterial1 bacterial-genome-analysis1 bacterial-genomes1 bamtofastq1 bases2fastq1 BBduk1 bbmap1 bcl2fastq1 Beacon1 Behavioral data1 benchamrking1 benchmark1 benchmarking1 bgc1 Big-data1 BioBB1 bioformats1 bioformats2raw1 Bioimage1 Bioinformatics tool1 Biomedical Ontologies1 BioScanEurope1 BioStudies1 biosynthetic-gene-clusters1 bisulfite-sequencing1 Bootstrapping1 bowtie21 BQSR1 braken1 Braker31 bustools1 bwa-mem21 carveme1 CATH1 causal inference1 cBioPortal1 cell-lines1 cfDNA1 chimeric-alignment1 Chinese-language1 Chowell_train_test1 chromatin-accessibiity1 chromatin-immunoprecipitation1 chromosome-conformation-capture1 circle-seq1 circular1 clip1 clip-seq1 Clustering1 cmip61 common data model1 community-detection1 Community_metrics1 comparative effectiveness1 comparative-genomics1 Comparison1 Compomics1 Connectome-based predictive modeling1 container1 contamination1 contigs1 coprolite1 corruption1 cosmic1 counts1 covid191 CPM1 cramtofastq1 crispr1 crispr-analysis1 crispr-cas1 cross-validation1 cryosparc1 ctat1 Cut&run1 cutandrun1 cutandrun-seq1 cutandtag1 cutandtag-seq1 CUTnRUN1 CWR1 cytometry1 Darwin core1 data annotation1 data fusion1 data integration1 Data package1 data retrieval and transformation1 data transformation1 data wrangling1 data-cleaning1 data-independent-proteomics1 data-recovery1 DataOne1 dda1 ddbj1 DE1 de novo1 de-identification1 decontamination1 deep-learning1 deep-variant1 Deeplearning1 demo1 denovo1 deseq21 dia1 dia-proteomics1 diagnostics1 DIAMOND1 Diff1 differential expression1 differential-abundance1 differential_expression1 Digital Twin1 Digitalhumanities1 directed acyclic graph1 disease outcome prediction1 DL1 dna barcoding1 dna-methylation1 Docker1 Domain-Domain interaction1 dot-plot1 download1 draft1 dRNAseq1 drug discovery1 drug-response1 drug-response-prediction1 drugs1 dualrna-seq1 durg response simulation1 earth-observation1 Earthquake Detection1 eccdna1 ecdna1 Ecological metadata language1 eFlows4HPC1 EGA-archive1 elementbiosciences1 em-seq1 emergen_validated1 EML1 eml-annotation1 ena1 eosc-nordic1 epigenome1 epitope1 epitope-prediction1 eukaryotes1 Evaluation1 evolutionary-tree1 Expospomics1 extrachromosomal-circular-dna1 EZyRB1 facs-sorting1 fair-principles1 fastp1 fastq-corrupted1 fastq-format1 fcs1 featurecounts1 file conversion1 filter1 filtering1 fish1 fMRI1 Fnn1 Formulaassignment1 Fragmentomics1 function1 Fungi1 fusion1 fusion-genes1 Galaxy-E1 GATK1 GATK31 GEM1 gene expression analysis1 gene expression correlation1 gene expression data wrangling1 Gene ontology term sets similarity1 Gene Prioritization1 gene-expression1 gene-fusion1 generalization1 genetic design1 Genomeannotation1 genomic ancestry1 genomics-visualization1 genotype1 geo1 geo database mining1 Geosciences1 ggbio1 GLM1 global assemblies1 gnomad1 gnps1 google1 graph1 Gravitational Waves1 GRIDS1 GRIDSS1 GRN1 gro-seq1 gsea1 GTF1 GUI1 HaplotyeCaller1 hicar1 high-throughput1 high-throughput_sequencing_analysis1 hla-typing1 hmdb1 horizontal-gene-transfer1 host-pathogen1 host-pathogen PPIs1 HTSeq1 Humanities1 humann21 Hybrid Workflow1 hybrid-assembly1 hyperparameter-tuning1 IA1 IDR1 Iedb1 image file format1 image-analysis1 image-segmentation1 imageanaylsis1 imageJ1 Imagerecognition1 immcantation1 immunology1 immunopeptidomics1 immunorepertoire1 imputation1 index1 international comparison1 Introductions1 iontorrent1 isoform switching1 isoseq1 isoseq-31 iwc1 Iwtomics1 Jbrowse1 Juicer1 kmeans1 kmer1 kmer-counting1 kmer-frequency-count1 kraken21 Kratos Multiphysics1 krona1 Labbook1 label-free-quantification1 landsat1 last1 lfq1 LiftOver1 limma1 linked-reads1 Llr6_model1 Logistic_regression_model1 long-read1 Loris1 Lotus21 low-pass-sequencing1 Ludwig1 Luigi & Rufus workflow1 machine-learning1 macs21 MAG1 Magic1 map1 Marine omics1 mass-spec1 massbank1 MaxQuant1 memote1 metagenomes1 Metaplasmidome1 methyl-seq1 MGE1 mhc1 mhc-binding-prediction1 microarray1 microscopy1 minimal-example1 miniTurboID1 Mirna1 Mito-flash1 Mitochondrion_tracking1 mlxv1 mnase-seq1 Mnist1 Mobilome1 model1 Modeling1 ModGP1 molecular-pixelation1 molecularcartography1 Moleculardynamics1 mpvx1 MRI1 ms11 ms21 Multivariate1 Mutect21 n501 name:amplicon1 Name:bacsnp1 Name:baculoviridae1 Name:baculovirus1 Name:circos1 Name:data-management1 Name:deconvolution1 Name:gtn1 Name:naldv1 Name:nanopore1 name:PROFILING1 Name:sequenceanalysis1 Name:single_cell1 Name:viz1 nanostring1 nanostringnorm1 nascent1 natural-products1 ncbi sra1 ndvi1 networks1 NGFF1 Noiseestimation1 non-coding1 non-model1 Non-parametric1 nonspliced1 Nord31 NS31 nucleosome1 nucleosome-maps1 nucleosome-positioning1 observation1 OME-TIFF1 openebench1 optitype1 oxford-nanopore1 pairwise-alignment1 parallel1 Parsl1 pathogen-genomics1 pathogenicity score1 Pathology1 Pathway co-occurrence1 pbat1 peptides1 Perl1 Permeability1 personalized-medicine1 Pfam1 phylogenetic-placement1 pixelator1 pixelgen-technologies1 Plant1 pod51 polygenic risk score1 polygenic score1 population-genetics1 pox1 pre-processing1 prediction1 Presence_absence1 pro-seq1 prokaryotes1 prokka1 Proline1 Protein domains1 protein interactin data triplification1 protein interactions database integration1 protein-databases1 protein-families1 protein-fold-prediction1 protein-folding1 Protein-Protein Interaction1 Protein-Protein interaction prediction1 protein-sequences1 proteins1 proteins network augmentation1 Pseudobulk1 public cancer datasets exploration1 Published1 Pubmed1 Pubtator1 puretarget1 purge_dups1 pypgatk1 qiime21 qPCR1 QTL mapping1 quantseq1 R-package1 radio interferometry1 randomization-tests1 rare-disease1 RDF1 rdkit1 readmapping1 reads-interleaving1 reads_selection1 reads_simulation1 Recalibration1 Reconstruction1 recovery-tool1 Reduced Order Modeling1 Regression1 Regulatory Mendelian Mutation score1 RELIANCE1 ReMM1 repeat1 repseq1 rice1 rna-rbp-interactions1 robustness-assessment1 rrbs1 rrna1 RSeQC1 salmon1 sambamba1 satellite-imagery1 screening1 SDM1 secondary-metabolites1 Seismic Detection1 Semantic Comparison1 Semantic Interpretation1 semantic web standards1 Sempi31 sentinel-2 data1 sequence search1 sequence-classification1 shiny1 short-reads1 SIM1 single particle analysis1 single-cell-omics1 single-end1 SKA1 slamseq1 small-rna1 smart-seq 21 Smfish1 smoove1 smrna-seq1 Solid Earth1 SPARK1 spatial1 Species abundance1 spectra1 spectral-unmixing1 splicing1 sra1 strandedness1 StringTie1 survivor1 SV1 synapse1 TAD1 tama1 target-panels1 taxonomies1 taxonomy1 tcga1 TELLSeq1 telomere1 Text1 Text-mining1 Text_mining1 tiddit1 tidyverse1 tmt1 Tomography1 topologically associating domains1 Toxicology1 trajectories1 Trans-Proteomic1 transcription1 Transcription Start Sites1 transcriptional-dynamics1 tree1 trend-analysis1 trends1 trimming1 tss1 tumour1 ultra1 umi1 umis1 Unicycler1 unique-molecular-identifier1 unpaired-reads1 urgent computing1 vaccines1 validaiton o protein interaction predictions1 variant1 variant pathogenicity prediction1 variant-annotation1 VGP_curated1 viral1 viral-integration1 viruses1 virusintegrationfinder1 Voronoi1 well-formed1 whole-exome-sequencing1 whole-genome-alignment1 whole-genome-sequencing1 wnt signaling1 worflow1 XNAT1 More...

GTN Bot337 WorkflowHub Bot174 Genís Bayarri70 Raül Sirvent33 Anna Syme25 Diego De Panis18 Bert Droesbeke16 Laura Rodriguez-Navas14 Sarah Williams14 Daniel Clarke13 Yvan Le Bras12 Ambarish Kumar10 Bart Nijsse10 Anne Fouilloux9 Tracy Chew9 Cristóbal Gallardo9 Georgina Samaha8 Jean-Marie Burel8 Miguel Vazquez8 Cristian Tatu8 Fernando Vázquez-Novoa8 Paul De Geest8 Douglas Lowe7 Yasmmin Martins7 W. Daniel Kissling7 Johan Gustafsson6 Martin Beracochea5 Jasper Koehorst5 Sergi Sayols5 Helena Rasche5 Oliver Woolland5 Tom Brown5 Matthieu Muffato5 Aldar Cabrelles5 Melchior du Lac4 Willem de Koning4 Peter van Heusden4 johan Rollin4 Dennis Dollée4 Konstantinos Kyritsis4 Bryan Raubenolt4 Nicolò Giacomini4 Riccardo Massei4 Stian Soiland-Reyes3 Irene Sánchez3 Juma Bayjan3 Valentine Murigneux3 Mike Thang3 Wolfgang Maier3 Anton Nekrutenko3 Jeanette Reinshagen3 Varsha Kale3 Pablo Riesgo Ferreiro3 Daniel Marchan3 Damon-Lee Pointon3 Kateřina Storchmannová3 Oliver White3 Timon Schlegel3 Marie Jossé3 Hervé Ménager2 Luca Pireddu2 Robin Long2 Beatriz Serrano-Solano2 Pavankumar Videm2 Simone Leo2 Ross Thorne2 Sarah Beecroft2 Volodymyr Savchenko2 Johannes Köster2 thodk2 Elida Schneltzer2 Pasi Korhonen2 Miguel Roncoroni2 Kary Ocaña2 Cristiane Taniguti2 Peter Menzel2 Adam Tofilski2 Simon Rolph2 David James Sherman2 Stevie Pederson2 Tina Tian2 Daan Hazelaar2 Andrea Furlani2 Vasiliki Panagi2 Khaled Jum'ah2 Fabrice Touzain2 Johannes Kemper2 Jorge Ejarque2 Rutger Vos2 Nathaniel Matteson2 Aishwarya Iyer2 Ashish Bhawel2 Xiaolong Luo2 Kristina Gomoryova2 Sora Yonezawa2 Diana Chiang Jurado2 Pauline Seguineau2 Panna Lukacs2 Oleg Kalashev2 SaibotMagd magd2 Jiamian He2 Dan Parsons2 Daniel Del Hoyo2 francois moreews1 Camille Juigné1 Laura del Cano1 Ivan Topolsky1 ignacio eguinoa1 Andrea Giachetti1 Michael R. Crusoe1 Matteo Chiara1 Carlos Oscar Sorzano Sanchez1 Paul Brack1 phytopat gembloux1 johan Rollin1 Marco De La Pierre1 Julian Uszkoreit1 Qinqin Long1 Dennis Hendriksen1 Daphne Wijnbergen1 Patrick Durand1 Cyril Noel1 Richard Lupat1 Javier Moldon1 Bianca Pasat1 Rob Edwards1 Valentin Tilloy1 Michael Roach1 Ryan Patterson-Cross1 Alexander Botzki1 [email protected] Panou1 Haris Zafeiropoulos1 Kaur Alasoo1 Hrishikesh Dhondge1 Marvin Martens1 Marlene Rezk1 Naga Kasinadhuni1 Casper de Visser1 Radek Veverka1 Tim Booth1 Samuel Lambert1 Ekaterina Sakharova1 Alejandra Escobar1 Saskia Hiltemann1 bugra oezdemir1 Max Schubach1 Luc Cornet1 Silas Kieser1 Felicita Gernhardt1 Nico Trummer1 Ang Guo1 Diego Garrido-Martín1 Roderic Guigó1 Bruno P. Kinoshita1 Luca Cozzuto1 Xiaokang Zhang1 Zavolan Lab1 Mahnoor Zulfiqar1 Jeffrey Detras1 Thomas Gruber1 Marjan Meurisse1 Ben Price1 Jorrit Mesman1 Elisabetta Spinazzola1 Rosa M Badia1 Anand Maurya1 Agata Kilar1 Vincent Hervé1 Markus Konkol1 Jessica Gomez-Garrido1 Akshay Akshay1 Phuong Doan1 Davide Gurnari1 David Yuan1 Justin Sonneck1 Daniele Lezzi1 Yi Sun1 Bram Danneels1 Zafran Hussain Shah1 Denys Savchenko1 Magdalena Antczak1 Michael Hall1 Rafael Terra1 Ziad Al-Bkhetan1 Dominik Lux1 Archit Dabral1 Andrii Neronov1 Michael Lloyd1 Arnau Soler Costa1 Thomas Roetzer-Pejrimovsky1 Helge Hecht1 Wudmir Rojas1 David Potesil1 Carlos Classen1 Usman Rashid1 Jinhu Wang1 dan rick1 Pavel Akhtyamov1 Francesco Messina1 Sebastian Röner1 Ann-Kathrin Dörr1 仕卓 张1 Mahesh Binzer-Panchal1 Michael Lynch1 Jen-Hung Wang1 Fabian Hausmann1 Qiang Ye1 Liang Cheng1 Benjamin Istace1 Alberto Aguado1 YIN ZHANG1 Kisaru Liyanage1 Kieran Atkins1 Tobias Bachmann1 Tristan Pelser1 Albert Puiggros1 Daniel Bauer1 Zhi Song1 Viola Fanfani1 Lorenz Gruber1 zhantian xu1 Natasha Clarke1 Jonas Kasmanas1 Zhen Zhang1 Andrei Variu1 Tyler Lovelace1 Jeanne Chèneby1 Robin Navest1 Avani Bhojwani1 Yichao Hua1 Azusa Kubota1 More...

Galaxy Training Network350 Intergalactic Workflow Commission (IWC)91 nf-core83 BioBB Building Blocks80 Australian BioCommons44 Workflows and Distributed Computing42 Galaxy Australia30 ERGA Assembly23 usegalaxy-eu22 GalaxyProject SARS-CoV-221 QCIF Bioinformatics20 Sydney Informatics Hub17 UNLOCK15 COMPSs Tutorials14 NIH CFDE Playbook Workflow Partnership13 PNDB12 EuroScienceGateway12 eFlows4HPC general11 MGnify9 Galaxy Climate9 OME8 PerMedCoE8 IBISBA Workflows7 yPublish - Bioinfo tools7 Biodiversity Genomics Europe (general)7 Laserfarm applications to European demonstration sites7 CWL workflow SARS-CoV-26 Integrated and Urban Plant Pathology Laboratory6 EJPRD WP13 case-studies workflows6 HoloFood at MGnify6 Tree of Life Genome Analysis6 EGA6 IMBforge5 UX trial team5 iPC: individualizedPaediatricCure5 Specimen Data Refinery5 Cluster Emergent del Cervell Humà5 Seq4AMR5 Scipion CNB5 EOSC4Cancer5 NanoGalaxy4 SANBI Pathogen Bioinformatics4 Biodata Analysis Group4 Tree of Life Genome Assembly4 Generalized Open-Source Workflows for Atomistic Molecular Dynamics Simulations of Viral Helicases4 UFZ - Image Data Management and Processing Workflows4 SARS-CoV-2 Data Hubs3 Snakemake-Workflows3 ODA3 CO2MICS Lab3 EU-Openscreen3 TRON gGmbH3 TRE-FX3 Euro-BioImaging3 ERGA Annotation3 Bioinformatics Laboratory for Genomics and Biodiversity (LBGB)3 BY-COVID (general)3 Chemical Data Lab3 NHM Clark group3 Proteomics CEITEC3 FAIR-EASE3 iBOL Europe Museum Skimming3 nf-core viralrecon2 V-Pipe2 EOSC-Life - Demonstrator 7: Rare Diseases2 Pawsey Supercomputing Research Centre2 SeBiMER2 Applied Computational Biology at IEG/HMGU2 INFRAFRONTIER workflows2 TransBioNet2 CRC Cohort2 Workflows Australia2 Medizinisches Proteom-Center, Medical Bioinformatics2 usegalaxy.be workflows2 Air Quality Prediction2 Read2Map2 ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression2 KircherLab2 Apis-wings2 BioDT Use Case 4.1.1.2 Ecosystem services2 MISTIC2 BSC-CES2 Black Ochre Data Labs2 Workflows for geographic science2 Katdetectr2 ANSES-Ploufragan2 WP7 - Earthquakes2 Pillar III: Urgent computing for natural hazards2 CholGen2 Peter Menzel's Team2 Genome Data Compression Team2 RECETOX SpecDatRI2 bonohulab2 Astroparticle Lab2 BioImage Informatics and Analysis Workflows2 CDPP2 FAIR_thesis: Marine acoustic data2 NMR Workflow1 COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource1 Italy-Covid-data-Portal1 EOSC-Life-WP6-Demos1 EOSC-Life WP31 MOLGENIS1 Janis1 IAA-CSIC1 FAME1 CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus1 HecatombDevelopment1 OpenEBench1 Bioinformatics and Biostatistics (BIO2 ) Core1 VIB Bioinformatics Core1 Single Cell Unit1 emo-bon1 CINECA1 Toxicology community1 Gyn Department1 AGRF BIO1 X-omics1 CAPSID1 Edinburgh Genomics1 NBIS1 BCCM_ULC1 Computational Science at HZDR1 Big data in biomedicine1 Guigó lab1 Statistical genetics1 Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation1 Bioinformatics Unit @ CRG1 ELIXIR Proteomics1 IRRI Bioinformatics Group1 Zavolan Lab1 Metabolomics-Reproducibility1 NGFF Tools1 Bioinformatics workflows for life science1 Helmholtz Scientific Project Workflow Platform1 BY-COVID Baseline Use Case: SARS-CoV-2 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection1 Lake Erken modelling setup1 EOSC-Life WP3 OC Team, cross RI project1 ARA-dev1 Mendel Centre for Plant Genomics and Proteomics1 WP5 - Volcanoes1 WP6 - Tsunamis1 Metagenomic tools1 Pillar I: Manufacturing1 Polygenic Score Catalog1 MLme: Machine Learning Made Easy1 Dioscuri TDA1 MMV-Lab1 EMBL-CBA1 EBP-Nor1 Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data1 Pangenome database project1 HP2NET - Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment1 Building spatio-temporal workflows in Galaxy1 CEMCOF1 Jackson Laboratory NGS-Ops1 BRAIN - Biomedical Research on Adult Intracranial Neoplasms1 Institute for Human Genetics and Genomic Medicine Aachen1 Plant-Food-Research-Open1 WGGC1 ELIXIR Metabolomics1 Medvedeva Lab1 16S rRNA Analysis1 Protein-protein and protein-nucleic acid binding site prediction research1 Culhane Lab1 IDUN - Drug Delivery and Sensing1 ErasmusMC Clinical Bioinformatics1 MAXOMOD1 NkuyfqLab1 EnrichDO1 Application Security - Test Crypt4GH solutions1 RenLabBioinformatics1 National Computational Infrastructure (NCI) WorkflowHub team1 Into the deep1 CPM1 Research Data Management ICE-21 LiDAR1 Senckenberg Digital Collection and Biodiversity Information Technologies1 QuackenbushLab1 Virus sequencing team1 SOS1 CSUbioinformatics1 SIMEXP1 Kasmanas1 Structural Variation Analysis1 CausalCoxMGM Team1 CrustyBase1 Applied Computational Cancer Research1 Click-qPCR1 More...

Galaxy350 Independent Teams314 nf-core83 BioExcel80 Australian BioCommons75 eFlows4HPC60 COVID-19 Biohackathon31 ERGA26 ELIXIR16 Sanger Tree of Life8 Biodiversity Genomics Europe (BGE)7 EcoLiDAR - ecological applications of LiDAR point clouds7 HoloFood6 DISSCo - Distributed System of Scientific Collections5 EOSC4Cancer5 A Digital Twin for GEOphysical extremes (DT-GEO)4 EOSC-Life3 BioDT3 Proteomics CEITEC3 iBOL Europe3 ELIXIR Belgium2 GenomeDataCompression2 EIRENE-CZ2 Hiroshima workflow community2 EOSC-Life-WP61 BeYond-COVID (BY-COVID)1 JKU 1 IRRI-Bioinformatics1 HELIPORT1 Coupled Catchment Lake Modelling1 AquaINFRA1 WGGC1 IKIM 16S Analysis1 MAXOMOD1 NkuyfqLab_Space1 More...

Adam Hospital76 Genís Bayarri75 Anna Syme24 Diego De Panis18 Bart Nijsse15 Jasper Koehorst14 Tracy Chew13 Yvan Le Bras11 Georgina Samaha11 Laura Rodriguez-Navas9 Rosemarie Sadsad9 Raül Sirvent9 Martin Beracochea8 Jean-Marie Burel8 Cristian Tatu8 Delphine Lariviere7 Saskia Hiltemann7 Javier Conejero7 Jinhu Wang7 W. Daniel Kissling7 Douglas Lowe6 José Mª Fernández6 Paul Zierep6 Coline Royaux5 Sergi Sayols5 Aldar Cabrelles5 Melchior du Lac4 Friederike Ehrhart4 Gareth Price4 Oliver Woolland4 Cali Willet4 Jorge Ejarque4 Bryan Raubenolt4 Riccardo Massei4 Ambarish Kumar3 Pavankumar Videm3 Wolfgang Maier3 Juma Bayjan3 Ozan Ozisik3 Valentine Murigneux3 Patrick Durand3 Laura Leroi3 Mike Thang3 Laurence Livermore3 Germán Royval3 Cristóbal Gallardo3 Cenna Doornbos3 Jeanette Reinshagen3 Ekaterina Sakharova3 Tom Brown3 Konstantinos Kyritsis3 Rosa M Badia3 Damon-Lee Pointon3 Ivan Topolsky2 Luca Pireddu2 Anne Fouilloux2 Michael R. Crusoe2 Julian Uszkoreit2 Helena Rasche2 Alexandre Cormier2 Cyril Noel2 Pierre Cuzin2 Volodymyr Savchenko2 Philipp Gormanns2 Anthony Bretaudeau2 Kary Ocaña2 Varsha Kale2 Tatiana Gurbich2 Cristiane Taniguti2 Peter Menzel2 Diego Garrido-Martín2 Roderic Guigó2 Stevie Pederson2 Andrea Furlani2 Ben Price2 Johannes Kemper2 Phuong Doan2 Denys Savchenko2 Kateřina Storchmannová2 Changlin Ke2 Ziad Al-Bkhetan2 Helge Hecht2 Kristina Gomoryova2 Zargham Ahmad2 Nicolò Giacomini2 Sora Yonezawa2 Marie Jossé2 Pauline Seguineau2 Dan Parsons2 Stian Soiland-Reyes1 Camille Juigné1 Krzysztof Poterlowicz1 Willem de Koning1 Pau Andrio1 Johan Gustafsson1 Peter van Heusden1 Matthias Haimel1 Carlos Oscar Sorzano Sanchez1 Paul Brack1 Sarah Beecroft1 Marco De La Pierre1 Richard Lupat1 Johannes Köster1 Valentin Tilloy1 Michael Roach1 Elida Schneltzer1 Luiz Gadelha1 Asier Gonzalez-Uriarte1 Wolfgang Maier1 Woosub Shin1 Ryan Patterson-Cross1 Haris Zafeiropoulos1 Hrishikesh Dhondge1 Kim Philipp Jablonski1 Pasi Korhonen1 Marvin Martens1 Tazro Inutano1 Marlene Rezk1 Casper de Visser1 Anton Nekrutenko1 Jasper Ouwerkerk1 Benjamin Wingfield1 Anna Niehues1 Marie-Dominique Devignes1 Tim Booth1 Samuel Lambert1 Alejandra Escobar1 Katherine Farquharson1 Dennis Dollée1 Lucas Cruz1 Pablo Riesgo Ferreiro1 Felicita Gernhardt1 Andrey Prjibelski1 Xiaokang Zhang1 Zavolan Lab1 Mahnoor Zulfiqar1 Veit Schwämmle1 Anton Korobeynikov1 Luiz Gadelha1 Vasiliki Panagi1 Khaled Jum'ah1 Jorrit Mesman1 Elisabetta Spinazzola1 Agata Kilar1 Jessica Gomez-Garrido1 Sagane Joye-Dind1 Akshay Akshay1 Davide Gurnari1 David Yuan1 Justin Sonneck1 Daniele Lezzi1 William Eagles1 Zafran Hussain Shah1 Fernando Vázquez-Novoa1 Nandan Deshpande1 Michael Hall1 Rafael Terra1 Ian Brennan1 Aishwarya Iyer1 Dominik Lux1 Bérénice Batut1 Ashish Bhawel1 Daniel Bauer1 Andrii Neronov1 Amy Curwin1 Arnau Soler Costa1 Thomas Roetzer-Pejrimovsky1 Xiaolong Luo1 Elliott J. Price1 Wudmir Rojas1 David Potesil1 Carlos Classen1 Jordi Rambla1 Timon Schlegel1 Pavel Akhtyamov1 Francesco Messina1 Sebastian Röner1 Ann-Kathrin Dörr1 仕卓 张1 Mahesh Binzer-Panchal1 Martin Pippel1 Jen-Hung Wang1 Fabian Hausmann1 Qiang Ye1 Birgit Rijvers1 Liang Cheng1 Benjamin Istace1 Kisaru Liyanage1 Matthew Downton1 Jean-Marc Aury1 Caroline Belser1 Kieran Atkins1 Tobias Bachmann1 Albert Puiggros1 Mitchell O'Brien1 Cedric Bhihe1 Georgina Díez1 Viola Fanfani1 Lorenz Gruber1 Katerina Hanakova1 Romane Libouban1 Natasha Clarke1 Jiamian He1 Lune Bellec1 Jonas Kasmanas1 Ryo Nozu1 Robin Navest1 More...

BioCommons ‘Bring Your Own Data’ Expansion Project39 Interactive Jupyter Notebooks for FAIR and reproducible biomolecular simulation workflows17 Tutorials for BioExcel Building Blocks (BioBB)11 BY-COVID related workflows11 Workflows in EuroScienceGateway10 scRNAseq processing in galaxy8 COMPSs Workflows from 2024 Tutorial8 TSI annotation workflows7 ERGA Assembly Galaxy Long Reads & Hi-C Pipelines (Hifiasm-solo + Purge_Dups + YaHS)7 Freely accessible ready to use global infrastructure and workflows for SARS-CoV-2 monitoring6 IDR6 ERGA Assembly Galaxy HiFi & HiC Pipelines (Hifiasm-HiC + Purge_Dups + YaHS)6 16S Microbial Analysis with mothur (on Galaxy Australia)6 ERGA Assembly Galaxy ONT+Illumina & HiC Pipelines (NextDenovo-HyPo + Purge_Dups + YaHS)6 ERGA Assembly Galaxy ONT+Illumina & HiC Pipelines (Flye-HyPo + Purge_Dups + YaHS)6 BioExcel Building Blocks (BioBB) Protein MD Setup Tutorials5 EuCanImage FHIR ETL Implementation5 HiFi genome assembly on Galaxy4 Vertebrate Genomes Pipelines (VGP) workflows3 CEITEC CryoEM Facility Workflows3 ERGA Assembly Snakemake HiFi & HiC Pipelines3 Genome Evaluation for ERGA-BGE Reports3 Genome Assembly Workflows for ERGA-BGE genomes3 TronFlow2 Sanger Tree of Life Assembly method1 More...

Bioinformatics35 Whole genome sequencing26 Sequence assembly23 Genetic variation19 Genomics18 Transcriptomics17 Metagenomics14 Ecology12 Biodiversity11 Biomedical science11 Computer science10 Gene expression9 Population genomics9 Imaging7 Bioimaging6 Data management6 Data mining6 Sequence analysis6 Workflows6 Machine learning5 Metagenomic sequencing5 Oncology5 Compound libraries and screening4 Copy number variation4 Gene transcripts4 Microbiology4 Sequencing4 Computational biology3 Data integration and warehousing3 Data quality management3 DNA mutation3 DNA polymorphism3 Drug discovery3 Genetics3 Preclinical and clinical studies3 Protein interactions3 Proteomics3 Sample collections3 Virology3 Cell biology2 Cheminformatics2 Computational chemistry2 Data curation and archival2 Data visualisation2 Environmental sciences2 Exome sequencing2 Gene structure2 Infectious disease2 Mapping2 Molecular interactions, pathways and networks2 Pharmacology2 Physics2 Protein interaction experiment2 Quantitative genetics2 Rare diseases2 Structural variation2 Agricultural science1 ChIP-seq1 Comparative genomics1 DNA packaging1 Epigenomics1 Function analysis1 Functional genomics1 Human genetics1 Marine biology1 Medical imaging1 Medical informatics1 Medicinal chemistry1 Metabolomics1 Metatranscriptomics1 Microbial ecology1 Molecular genetics1 Nucleic acid sites, features and motifs1 Ontology and terminology1 Pathology1 Phylogenetics1 Phylogenomics1 Phylogeny1 Protein binding sites1 Protein folds and structural domains1 Protein structure analysis1 Protein variants1 Proteins1 Proteomics experiment1 Public health and epidemiology1 Small molecules1 Statistics and probability1 Structural genomics1 Systems biology1 Taxonomy1 More...

Genome assembly17 Sequencing quality control17 Variant calling12 Sequence assembly8 Expression analysis7 Variant filtering7 Annotation6 Sequence clustering6 Sequence alignment5 Taxonomic classification5 De-novo assembly4 Genome annotation4 Calculation3 Conversion3 Copy number variation detection3 Data retrieval3 Gene-set enrichment analysis3 Haplotype mapping3 Modelling and simulation3 Protein interaction network analysis3 Transcriptome assembly3 Variant classification3 Visualisation3 Antimicrobial resistance prediction2 Correlation2 Data filtering2 Differential gene expression profiling2 Gene functional annotation2 Genetic mapping2 Genome visualisation2 Image analysis2 Indel detection2 Prediction and recognition2 Protein interaction network prediction2 Scaffolding2 Sequence assembly validation2 Sequence assembly visualisation2 SNP annotation2 SNP detection2 Weighted correlation network analysis2 Binding site prediction1 Classification1 Clustering1 Contact map calculation1 Copy number estimation1 Data analysis1 Data handling1 Differential protein expression profiling1 Dimensionality reduction1 DNA barcoding1 Enrichment analysis1 Expression correlation analysis1 Feature extraction1 Format detection1 Gene expression profiling1 Genome alignment1 Genome analysis1 Genome comparison1 Global alignment1 ID mapping1 Information retrieval1 k-mer counting1 Local alignment1 Mapping1 Metabolic pathway prediction1 Named-entity and concept recognition1 Network analysis1 Nucleic acid property calculation1 Operation1 Pairwise sequence alignment1 Peptide identification1 Phasing1 Phylogenetic inference1 Protein identification1 Protein-protein interaction analysis1 Read mapping1 Relation extraction1 RNA-Seq analysis1 Sequence alignment analysis (site correlation)1 Sequence annotation1 Sequence contamination filtering1 Sequence cutting1 Sequence distance matrix generation1 Sequence profile generation1 Sequence trimming1 Single particle analysis1 Standardisation and normalisation1 Statistical calculation1 Statistical modelling1 Structural variation detection1 Structure-based sequence alignment1 Text annotation1 Text mining1 Transcription factor binding site prediction1 Validation1 More...

Stable350 Work-in-progress115 Deprecated9

Passing46 Not available14 All failing8