Workflows

fastp9 BWA7 MaBoSS7 Minimap27 PhysiCell7 BLAST6 FastQC6 Galaxy6 kraken26 BCFtools5 MultiQC5 shovill5 R4 SAMtools4 Seurat4 SPAdes4 taxonomy_krona_chart4 anndata3 Bowtie 23 BUSCO3 cisTEM3 Konstanz Information Miner (KNIME)3 MotionCor23 Scipion3 Variant Effect Predictor (VEP)3 BBMap2 CellProfiler2 ChiRA2 Cutadapt2 Flye2 MACS2 nanopolish2 NGSUtils2 picard_samtofastq2 PredPrIn2 QUAST2 SCANPY2 seqtk2 Snakemake2 SnpSift2 Unicycler2 VADR2 vardict2 vcfanno2 vcfutils2 XMIPP2 ABRicate1 AdapterRemoval1 AnnotSV1 Bandage1 BEDTools1 Bioconductor1 Biopython1 BlobToolKit1 BRAKER11 bx-python1 CARNIVAL1 cBioPortal1 CheckM1 clusterProfiler1 CNVkit1 COMBAT-TB Workbench1 decoupleR1 Delly21 DESeq21 Filtlong1 FLASH1 FreeBayes1 funannotate1 GADES1 Galaxy Image Analysis1 GATK1 gblocks1 GBMatch - GBMPredictor1 GenomeScope 2.01 GetOrganelle1 ggtree1 GSEA1 hAMRonization1 Hifiasm1 htseqcount1 ImageJ21 Infernal1 iqtree1 lofreq1 MAFFT1 Mash1 MaxBin1 Merqury1 Meryl1 MetaBAT 21 MitoHiFi1 MITOS1 MOB-suite1 MolMeDB1 NanoPlot1 ngsReports1 OBITools1 PhysiBoSS1 pilon1 PLINK1 Prodigal1 progeny1 protexcluder1 purge_dups1 QualiMap1 Racon1 RDKit1 RepeatMasker1 RepeatModeler1 scikit-image1 SemiBin1 seqkit1 SeqSero21 SISTR1 snippy1 STAR1 staramr1 StringTie1 TaxonKit1 tb-profiler1 Trim Galore1 varlociraptor1 VarScan1 WGCNA1 More...

Galaxy84 Common Workflow Language46 Nextflow34 Snakemake30 Python28 Jupyter11 KNIME9 Playbook Workflow Builder Workflow9 Workflow Description Language6 Bpipe5 COMPSs5 R markdown5 Scipion5 Autosubmit2 Docker2 Argo Workflow1 BioCompute Object1 Perl1 Pi1 Plug-in1 Rbbt1 Shell Script1 More...

Bioinformatics42 Genomics16 Galaxy12 imaging12 Nextflow12 Transcriptomics12 image processing11 Workflows11 Assembly10 covid-1910 CWL10 Annotation9 cancer9 Python8 rna-seq8 variant calling8 workflow8 Machine Learning7 SARS-CoV-27 bioimaging6 vgp6 Alignment5 bpipe5 FAIR workflows5 groovy5 Metagenomics5 nanopore5 pediatric5 Proteomics5 rna5 Snakemake5 Cheminformatics4 Climate4 copernicus4 helicase4 jupyter4 molecular dynamics4 OMERO4 ONT4 RDM4 Retrosynthesis4 rna virus4 SNPs4 spa4 variant_calling4 Virology4 antimicrobial resistance3 astronomy3 binning3 ChIP-seq3 Classification3 cryoem3 Databases3 Earth-system3 EOSC4Cancer3 FAIR3 generic3 genome_assembly3 Knime3 Ocean3 OME-Zarr3 Pathway Analysis3 pathway prediction3 rare diseases3 RNASEQ3 S33 SANBI3 scipion3 scRNA-seq3 Virus3 16S2 Amplicon2 AMR2 AMR-detection2 BGE2 Biodiversity2 CellProfiler2 CODEX22 coronavirus2 cosifer2 covid19.galaxyproject.org2 dengue2 DE_NOVO2 earth observation2 Electron microscopy2 Epigenomics2 ExomeDepth2 exploration2 gene set enrichment analysis2 genome2 Genome assembly2 Germline2 Glacios2 GWAS2 identification2 illumina2 kallisto2 kraken2 linkage_map2 manta2 MERS2 metabolic engineering2 Metabolomics2 metagenome2 microbial2 mirna prediction2 name:ONT2 NGS2 NSP132 pangeo2 pathogen2 pathway design2 personalized medicine2 Pipeline2 protein2 quality control2 Report2 scATAC-seq2 Semantic Network Analysis2 sequence annotation2 STAR2 Statistics2 structural variants2 Synthetic Biology2 TalosArctica2 TitanKrios2 TransBioNet2 WDL2 west nile2 zika2 10.3390/microorganisms100202921 18S1 ABR1 adaptor1 air-quality1 Alternative splicing1 annotsv1 ARTIC1 automated workflows1 BAM1 bash1 Behavioral data1 benchamrking1 benchmarking1 bioformats1 bioformats2raw1 Bioimage1 Bioinformatics tool1 Biomedical Ontologies1 BioScanEurope1 BioStudies1 blast1 bowtie21 BUSCO1 BWA1 C++1 carveme1 CATH1 Cellranger1 cfDNA1 cmip61 CNVkit1 community-detection1 Community_metrics1 Compomics1 Connectome-based predictive modeling1 contamination1 Conversion1 Copy Number Variation1 CPM1 cryosparc1 Darwin core1 data annotation1 data fusion1 data integration1 Data package1 data retrieval and transformation1 data transformation1 data wrangling1 DataOne1 Deep learning1 disease outcome prediction1 DL1 DNA-seq1 Domain-Domain interaction1 dRNAseq1 durg response simulation1 Ecological metadata language1 Ecology1 eDNA1 EGA-archive1 EML1 eml-annotation1 eosc-nordic1 epigenetics1 ERGA1 Evaluation1 fastp1 FastQC1 fcs1 featurecounts1 file conversion1 filtering1 fMRI1 Fragmentomics1 Galaxy-E1 GATK31 GATK41 GEM1 gene expression correlation1 gene expression data wrangling1 Gene ontology term sets similarity1 Gene Prioritization1 genetic design1 genome-annotation1 genomic ancestry1 geo database mining1 GLM1 gnps1 graph1 Gravitational Waves1 GRIDS1 GRIDSS1 GRN1 GTN1 GUI1 Hi-C1 high-throughput1 high-throughput_sequencing_analysis1 hmdb1 host-pathogen PPIs1 HPC1 IA1 image file format1 imageJ1 ITS1 Java1 k-mer1 Labbook1 LiftOver1 Luigi & Rufus workflow1 MAG1 Magic1 mapping1 Marine omics1 MARS-seq1 mass-spectrometry1 massbank1 MaxQuant1 memote1 Merqury1 Metabarcoding1 metatranscriptomics1 microbiome1 microscopy1 mlxv1 Modeling1 mpvx1 mpxv1 MRI1 Multi-omics1 MultiQC1 Multivariate1 n501 name:ILLUMINA1 name:public-data1 name:single-cell1 name:training1 ncbi sra1 ndvi1 networks1 NGFF1 non-coding1 Non-parametric1 nonspliced1 NS31 observation1 OME-TIFF1 openebench1 paired-end1 pangenome1 Parsl1 pathogenicity score1 Pathology1 Pathway co-occurrence1 Perl1 Permeability1 Pfam1 phasing1 phylogenetics1 pod51 polygenic risk score1 polygenic score1 prediction1 Presence_absence1 Proline1 Protein domains1 protein interactin data triplification1 protein interactions database integration1 Protein-Protein Interaction1 Protein-Protein interaction prediction1 proteins network augmentation1 public cancer datasets exploration1 QTL mapping1 quality1 radio interferometry1 RDF1 rdkit1 reads_selection1 reads_simulation1 Reconstruction1 Regulatory Mendelian Mutation score1 RELIANCE1 ReMM1 repeat1 sambamba1 SAMTools1 scientific publication text mining1 Semantic Comparison1 Semantic Interpretation1 semantic web standards1 sentinel-2 data1 sequence search1 SIM1 single particle analysis1 single-cell1 single-end1 SKA1 smart-seq 21 Species abundance1 spectra1 SV1 synteny1 taxonomy1 tcga1 telomere1 Tomography1 Toxicology1 Trans-Proteomic1 tuberculosis1 validaiton o protein interaction predictions1 variant1 variant pathogenicity prediction1 variation1 VCF1 wes1 WGS1 More...

Daniel Clarke13 Yvan Le Bras12 Bart Nijsse10 Laura Rodriguez-Navas9 Anne Fouilloux8 Jean-Marie Burel8 Miguel Vazquez8 Yasmmin Martins7 Cristóbal Gallardo6 Jasper Koehorst5 Sergi Sayols5 Aldar Cabrelles5 Melchior du Lac4 Willem de Koning4 Peter van Heusden4 johan Rollin4 Dennis Dollée4 Konstantinos Kyritsis4 Bryan Raubenolt4 Riccardo Massei4 Irene Sánchez3 Juma Bayjan3 Wolfgang Maier3 Anton Nekrutenko3 Jeanette Reinshagen3 Pablo Riesgo Ferreiro3 Daniel Marchan3 Kateřina Storchmannová3 Oliver White3 Timon Schlegel3 Marie Jossé3 Luca Pireddu2 Beatriz Serrano-Solano2 Pavankumar Videm2 Simone Leo2 Ross Thorne2 Volodymyr Savchenko2 Johannes Köster2 thodk2 Elida Schneltzer2 Pasi Korhonen2 Kary Ocaña2 Cristiane Taniguti2 Peter Menzel2 Adam Tofilski2 David James Sherman2 Stevie Pederson2 Tina Tian2 Daan Hazelaar2 Andrea Furlani2 Vasiliki Panagi2 Fabrice Touzain2 Nathaniel Matteson2 Aishwarya Iyer2 SaibotMagd magd2 Stian Soiland-Reyes1 Laura del Cano1 Douglas Lowe1 ignacio eguinoa1 Andrea Giachetti1 Michael R. Crusoe1 Matteo Chiara1 Carlos Oscar Sorzano Sanchez1 phytopat gembloux1 johan Rollin1 Julian Uszkoreit1 Helena Rasche1 Dennis Hendriksen1 Daphne Wijnbergen1 Patrick Durand1 Cyril Noel1 Javier Moldon1 Oliver Woolland1 Bianca Pasat1 Rob Edwards1 Valentin Tilloy1 Michael Roach1 Ryan Patterson-Cross1 Alexander Botzki1 [email protected] Panou1 Haris Zafeiropoulos1 Kaur Alasoo1 Hrishikesh Dhondge1 Marvin Martens1 Naga Kasinadhuni1 Casper de Visser1 Radek Veverka1 Tim Booth1 Samuel Lambert1 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 Tom Brown1 Elisabetta Spinazzola1 Anand Maurya1 Agata Kilar1 Vincent Hervé1 Akshay Akshay1 Phuong Doan1 Davide Gurnari1 David Yuan1 Justin Sonneck1 Yi Sun1 Bram Danneels1 Zafran Hussain Shah1 Denys Savchenko1 Michael Hall1 Rafael Terra1 Dominik Lux1 Michael Lloyd1 Arnau Soler Costa1 Thomas Roetzer-Pejrimovsky1 Carlos Classen1 Usman Rashid1 Jinhu Wang1 Pavel Akhtyamov1 Diana Chiang Jurado1 Sebastian Röner1 仕卓 张1 Mahesh Binzer-Panchal1 Michael Lynch1 Jen-Hung Wang1 Liang Cheng1 Benjamin Istace1 Alberto Aguado1 YIN ZHANG1 Kieran Atkins1 Tobias Bachmann1 Tristan Pelser1 Albert Puiggros1 Oleg Kalashev1 Zhi Song1 Viola Fanfani1 Lorenz Gruber1 zhantian xu1 Natasha Clarke1 Jonas Kasmanas1 More...

usegalaxy-eu21 UNLOCK15 NIH CFDE Playbook Workflow Partnership13 PNDB12 Galaxy Climate8 OME8 PerMedCoE8 IBISBA Workflows7 yPublish - Bioinfo tools7 Integrated and Urban Plant Pathology Laboratory6 EJPRD WP13 case-studies workflows6 EGA6 IMBforge5 UX trial team5 iPC: individualizedPaediatricCure5 Seq4AMR5 NanoGalaxy4 SANBI Pathogen Bioinformatics4 Biodata Analysis Group4 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 Scipion CNB3 Bioinformatics Laboratory for Genomics and Biodiversity (LBGB)3 Chemical Data Lab3 NHM Clark group3 FAIR-EASE3 SeBiMER2 Applied Computational Biology at IEG/HMGU2 INFRAFRONTIER workflows2 TransBioNet2 CRC Cohort2 Workflows Australia2 Medizinisches Proteom-Center, Medical Bioinformatics2 Air Quality Prediction2 Read2Map2 ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression2 KircherLab2 Apis-wings2 MISTIC2 BSC-CES2 Black Ochre Data Labs2 Workflows for geographic science2 Katdetectr2 ANSES-Ploufragan2 CholGen2 Peter Menzel's Team2 BioImage Informatics and Analysis Workflows2 CDPP2 NMR Workflow1 COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource1 Italy-Covid-data-Portal1 MOLGENIS1 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 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 Zavolan Lab1 Metabolomics-Reproducibility1 NGFF Tools1 Bioinformatics workflows for life science1 EOSC-Life WP3 OC Team, cross RI project1 ARA-dev1 Mendel Centre for Plant Genomics and Proteomics1 Metagenomic tools1 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 CEMCOF1 Jackson Laboratory NGS-Ops1 BRAIN - Biomedical Research on Adult Intracranial Neoplasms1 Institute for Human Genetics and Genomic Medicine Aachen1 Plant-Food-Research-Open1 Medvedeva Lab1 Protein-protein and protein-nucleic acid binding site prediction research1 Culhane Lab1 IDUN - Drug Delivery and Sensing1 ErasmusMC Clinical Bioinformatics1 EnrichDO1 Application Security - Test Crypt4GH solutions1 RenLabBioinformatics1 Into the deep1 CPM1 Research Data Management ICE-21 LiDAR1 Astroparticle Lab1 QuackenbushLab1 Virus sequencing team1 SOS1 CSUbioinformatics1 SIMEXP1 Kasmanas1 More...

Independent Teams302 EOSC4Cancer3 ELIXIR2 ERGA2 EOSC-Life1

Bart Nijsse15 Jasper Koehorst14 Yvan Le Bras11 Laura Rodriguez-Navas8 Jean-Marie Burel8 Delphine Lariviere6 Coline Royaux5 Sergi Sayols5 Aldar Cabrelles5 Melchior du Lac4 José Mª Fernández4 Friederike Ehrhart4 Bryan Raubenolt4 Riccardo Massei4 Juma Bayjan3 Ozan Ozisik3 Patrick Durand3 Laura Leroi3 Germán Royval3 Cenna Doornbos3 Jeanette Reinshagen3 Konstantinos Kyritsis3 Luca Pireddu2 Douglas Lowe2 Michael R. Crusoe2 Pavankumar Videm2 Julian Uszkoreit2 Alexandre Cormier2 Cyril Noel2 Pierre Cuzin2 Volodymyr Savchenko2 Philipp Gormanns2 Kary Ocaña2 Cristiane Taniguti2 Peter Menzel2 Diego Garrido-Martín2 Roderic Guigó2 Stevie Pederson2 Andrea Furlani2 Phuong Doan2 Denys Savchenko2 Kateřina Storchmannová2 Changlin Ke2 Marie Jossé2 Stian Soiland-Reyes1 Martin Beracochea1 Anne Fouilloux1 Matthias Haimel1 Carlos Oscar Sorzano Sanchez1 Helena Rasche1 Oliver Woolland1 Johannes Köster1 Valentin Tilloy1 Michael Roach1 Elida Schneltzer1 Luiz Gadelha1 Asier Gonzalez-Uriarte1 Woosub Shin1 Ryan Patterson-Cross1 Haris Zafeiropoulos1 Hrishikesh Dhondge1 Pasi Korhonen1 Marvin Martens1 Tazro Inutano1 Casper de Visser1 Benjamin Wingfield1 Anna Niehues1 Marie-Dominique Devignes1 Tim Booth1 Samuel Lambert1 Dennis Dollée1 Lucas Cruz1 Pablo Riesgo Ferreiro1 Felicita Gernhardt1 Xiaokang Zhang1 Zavolan Lab1 Mahnoor Zulfiqar1 Veit Schwämmle1 Luiz Gadelha1 Vasiliki Panagi1 Elisabetta Spinazzola1 Agata Kilar1 Akshay Akshay1 Davide Gurnari1 David Yuan1 Justin Sonneck1 Zafran Hussain Shah1 Michael Hall1 Rafael Terra1 Aishwarya Iyer1 Dominik Lux1 Amy Curwin1 Arnau Soler Costa1 Thomas Roetzer-Pejrimovsky1 Carlos Classen1 Jordi Rambla1 Timon Schlegel1 Pavel Akhtyamov1 Sebastian Röner1 仕卓 张1 Mahesh Binzer-Panchal1 Martin Pippel1 Jen-Hung Wang1 Birgit Rijvers1 Liang Cheng1 Benjamin Istace1 Jean-Marc Aury1 Caroline Belser1 Kieran Atkins1 Tobias Bachmann1 Albert Puiggros1 Viola Fanfani1 Lorenz Gruber1 Natasha Clarke1 Lune Bellec1 Jonas Kasmanas1 More...

IDR6 EuCanImage FHIR ETL Implementation5 CEITEC CryoEM Facility Workflows3 BY-COVID related workflows3 TronFlow2 Vertebrate Genomes Pipelines (VGP) workflows2 Workflows in EuroScienceGateway2 Genome Assembly Workflows for ERGA-BGE genomes2 More...

Bioinformatics23 Biodiversity10 Biomedical science9 Ecology9 Genetic variation8 Metagenomics7 Sequence assembly7 Bioimaging6 Biological databases6 Genomics6 Imaging6 Oncology5 Sequence analysis5 Data mining4 Transcriptomics4 Workflows4 Compound libraries and screening3 Data quality management3 Drug discovery3 Metagenomic sequencing3 Microbiology3 Preclinical and clinical studies3 Protein interactions3 Sample collections3 Sequencing3 Cheminformatics2 Data integration and warehousing2 Data submission, annotation and curation2 DNA polymorphism2 Machine learning2 Molecular interactions, pathways and networks2 Pharmacology2 Protein interaction experiment2 Proteomics2 Quantitative genetics2 Rare diseases2 Virology2 ChIP-seq1 Comparative genomics1 Computational biology1 Computer science1 Copy number variation1 Data visualisation1 DNA mutation1 Environmental science1 Epigenomics1 Gene expression1 Gene structure1 Gene transcripts1 Genetics1 Human genetics1 Infectious disease1 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 Physics1 Protein binding sites1 Protein folds and structural domains1 Protein variants1 Public health and epidemiology1 Structural variation1 More...

Variant calling6 Annotation5 Sequencing quality control5 Sequence assembly4 Data retrieval3 Gene-set enrichment analysis3 Protein interaction network analysis3 Variant classification3 Variant filtering3 Conversion2 Correlation2 Gene functional annotation2 Genome annotation2 Haplotype mapping2 Modelling and simulation2 Prediction and recognition2 Protein interaction network prediction2 SNP annotation2 Weighted correlation network analysis2 Analysis1 Antimicrobial resistance prediction1 Binding site prediction1 Calculation1 Classification1 Clustering1 Contact map calculation1 Copy number variation detection1 Data handling1 Differential gene expression profiling1 Dimensionality reduction1 DNA barcoding1 Enrichment analysis1 Expression correlation analysis1 Feature extraction1 Filtering1 Format detection1 Genome assembly1 ID mapping1 Image analysis1 k-mer counting1 Metabolic pathway prediction1 Named-entity and concept recognition1 Network analysis1 Nucleic acid property calculation1 Peptide identification1 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 distance matrix generation1 Sequence profile generation1 Single particle analysis1 Standardisation and normalisation1 Taxonomic classification1 Text annotation1 Text mining1 Transcription factor binding site prediction1 More...

Stable128 Work-in-progress63 Deprecated5

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