Workflows

BWA7 fastp7 MaBoSS7 PhysiCell7 BLAST5 Minimap25 BCFtools4 FastQC4 Galaxy4 kraken24 R4 Seurat4 shovill4 taxonomy_krona_chart4 Bowtie 23 cisTEM3 MotionCor23 MultiQC3 SAMtools3 Scipion3 SPAdes3 Variant Effect Predictor (VEP)3 CellProfiler2 ChiRA2 Cutadapt2 nanopolish2 NGSUtils2 picard_samtofastq2 PredPrIn2 seqtk2 SnpSift2 Unicycler2 VADR2 vardict2 vcfanno2 vcfutils2 XMIPP2 AdapterRemoval1 Bandage1 BBMap1 BEDTools1 Bioconductor1 BRAKER11 BUSCO1 bx-python1 CARNIVAL1 cBioPortal1 decoupleR1 Delly21 DESeq21 Filtlong1 FLASH1 Flye1 FreeBayes1 funannotate1 GATK1 htseqcount1 Infernal1 lofreq1 MACS1 MOB-suite1 ngsReports1 OBITools1 PhysiBoSS1 pilon1 PLINK1 progeny1 protexcluder1 Racon1 RepeatMasker1 RepeatModeler1 SeqSero21 SISTR1 STAR1 StringTie1 Trim Galore1 varlociraptor1 VarScan1 More...

Galaxy80 Common Workflow Language36 Nextflow27 Snakemake26 Python13 Jupyter11 Workflow Description Language6 Bpipe5 KNIME5 COMPSs5 Scipion5 R markdown3 Autosubmit1 Perl1 Pi1 Rbbt1 More...

Bioinformatics23 Galaxy12 Genomics11 Transcriptomics11 covid-1910 image processing10 Assembly9 Nextflow9 CWL8 imaging8 rna-seq8 workflow8 cancer7 Machine Learning7 Python7 variant calling7 Annotation6 SARS-CoV-26 vgp6 Alignment5 bpipe5 Climate5 genome-annotation5 groovy5 Metagenomics5 pediatric5 Proteomics5 rna5 astronomy4 copernicus4 helicase4 jupyter4 molecular dynamics4 nanopore4 ONT4 Retrosynthesis4 rna virus4 variant_calling4 Virology4 binning3 Classification3 cryoem3 Ecology3 EOSC4Cancer3 FAIR workflows3 generic3 OME-Zarr3 Pathway Analysis3 pathway prediction3 rare diseases3 RNASEQ3 S33 SANBI3 scipion3 scRNA-seq3 Snakemake3 SNPs3 spa3 Virus3 Workflows3 16S2 Amplicon2 antimicrobial resistance2 bioimaging2 CellProfiler2 Cheminformatics2 ChIP-seq2 CODEX22 coronavirus2 cosifer2 covid19.galaxyproject.org2 dengue2 DE_NOVO2 Electron microscopy2 Epigenomics2 ExomeDepth2 exploration2 gene set enrichment analysis2 genome_assembly2 Germline2 GWAS2 identification2 illumina2 kallisto2 kraken2 linkage_map2 manta2 MERS2 metabolic engineering2 Metabolomics2 mirna prediction2 name:ONT2 NSP132 pathway design2 personalized medicine2 Pipeline2 protein2 Semantic Network Analysis2 STAR2 structural variants2 Synthetic Biology2 TransBioNet2 WDL2 west nile2 zika2 10.3390/microorganisms100202921 18S1 ABR1 air-quality1 Alternative splicing1 AMR1 AMR-detection1 ARTIC1 automated workflows1 bash1 Behavioral data1 benchmarking1 BGE1 Biodiversity1 bioformats1 bioformats2raw1 Bioimage1 Biomedical Ontologies1 BioStudies1 blast1 bowtie21 BWA1 carveme1 CATH1 Cellranger1 cmip61 community-detection1 Community_metrics1 Compomics1 Conversion1 Darwin core1 data annotation1 data fusion1 data integration1 Data package1 data retrieval and transformation1 data transformation1 data wrangling1 Databases1 DataOne1 Deep learning1 disease outcome prediction1 DL1 DNA-seq1 Domain-Domain interaction1 dRNAseq1 durg response simulation1 earth observation1 Ecological metadata language1 eDNA1 EML1 eml-annotation1 eosc-nordic1 ERGA1 FAIR1 fastp1 FastQC1 featurecounts1 file conversion1 filtering1 Galaxy-E1 GATK31 GATK41 GEM1 gene expression correlation1 gene expression data wrangling1 Gene ontology term sets similarity1 Gene Prioritization1 genetic design1 genomic ancestry1 geo database mining1 GLM1 gnps1 Gravitational Waves1 GRIDS1 GRIDSS1 GTN1 GUI1 high-throughput1 high-throughput_sequencing_analysis1 hmdb1 host-pathogen PPIs1 HPC1 image file format1 imageJ1 ITS1 Knime1 LiftOver1 Luigi & Rufus workflow1 MAG1 mapping1 MARS-seq1 mass-spectrometry1 massbank1 MaxQuant1 memote1 Metabarcoding1 metagenome1 metatranscriptomics1 microbial1 microscopy1 mlxv1 Modeling1 mpvx1 mpxv1 Multi-omics1 MultiQC1 Multivariate1 name:ILLUMINA1 ncbi sra1 ndvi1 networks1 NGFF1 NGS1 non-coding1 Non-parametric1 nonspliced1 NS31 observation1 OME-TIFF1 openebench1 paired-end1 pangenome1 pangeo1 Parsl1 pathogenicity score1 Pathway co-occurrence1 Perl1 Permeability1 Pfam1 phylogenetics1 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 rdkit1 reads_selection1 reads_simulation1 Reconstruction1 Regulatory Mendelian Mutation score1 RELIANCE1 ReMM1 Report1 sambamba1 SAMTools1 scientific publication text mining1 Semantic Comparison1 Semantic Interpretation1 sentinel-2 data1 sequence annotation1 sequence search1 SIM1 single particle analysis1 single-end1 SKA1 smart-seq 21 Species abundance1 spectra1 Statistics1 SV1 tcga1 Tomography1 Toxicology1 Trans-Proteomic1 validaiton o protein interaction predictions1 variant1 variant pathogenicity prediction1 VCF1 More...

Yvan Le Bras11 Laura Rodriguez-Navas9 Anne Fouilloux8 Bart Nijsse8 Jean-Marie Burel8 Miguel Vazquez8 Paul De Geest8 Yasmmin Martins7 Cristóbal Gallardo6 Jasper Koehorst5 Sergi Sayols5 Melchior du Lac4 Willem de Koning4 johan Rollin4 Dennis Dollée4 Konstantinos Kyritsis4 Bryan Raubenolt4 Peter van Heusden3 Irene Sánchez3 Juma Bayjan3 Wolfgang Maier3 Anton Nekrutenko3 Jeanette Reinshagen3 Pablo Riesgo Ferreiro3 Daniel Marchan3 Oliver White3 Luca Pireddu2 Beatriz Serrano-Solano2 Pavankumar Videm2 Ross Thorne2 Volodymyr Savchenko2 Johannes Köster2 thodk2 Elida Schneltzer2 Pasi Korhonen2 Kary Ocaña2 Cristiane Taniguti2 Peter Menzel2 Adam Tofilski2 Tina Tian2 Daan Hazelaar2 Andrea Furlani2 Fabrice Touzain2 Nathaniel Matteson2 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 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 panou@fleming.gr Panou1 Haris Zafeiropoulos1 Kaur Alasoo1 Hrishikesh Dhondge1 Marvin Martens1 Naga Kasinadhuni1 Casper de Visser1 Samuel Lambert1 bugra oezdemir1 Max Schubach1 Luc Cornet1 Felicita Gernhardt1 Nico Trummer1 Ang Guo1 Diego Garrido-Martín1 Roderic Guigó1 Bruno P. Kinoshita1 Luca Cozzuto1 Xiaokang Zhang1 Zavolan Lab1 Mahnoor Zulfiqar1 Stevie Pederson1 Tom Brown1 Elisabetta Spinazzola1 Anand Maurya1 Agata Kilar1 Vincent Hervé1 Akshay Akshay1 Davide Gurnari1 David Yuan1 Daniel Clarke1 Justin Sonneck1 Yi Sun1 Bram Danneels1 Zafran Hussain Shah1 Denys Savchenko1 Kateřina Storchmannová1 Michael Hall1 Rafael Terra1 Dominik Lux1 Andrii Neronov1 More...

usegalaxy-eu14 UNLOCK13 PNDB11 EuroScienceGateway11 Galaxy Climate8 OME8 PerMedCoE8 IBISBA Workflows7 yPublish - Bioinfo tools7 Integrated and Urban Plant Pathology Laboratory6 IMBforge5 UX trial team5 iPC: individualizedPaediatricCure5 NanoGalaxy4 EJPRD WP13 case-studies workflows4 Seq4AMR4 Biodata Analysis Group4 Generalized Open-Source Workflows for Atomistic Molecular Dynamics Simulations of Viral Helicases4 SARS-CoV-2 Data Hubs3 ODA3 CO2MICS Lab3 EU-Openscreen3 TRON gGmbH3 Euro-BioImaging3 SANBI Pathogen Bioinformatics3 Scipion CNB3 NHM Clark group3 SeBiMER2 Snakemake-Workflows2 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 Apis-wings2 Workflows for geographic science2 Katdetectr2 ANSES-Ploufragan2 CholGen2 Peter Menzel's Team2 NMR Workflow1 COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource1 Italy-Covid-data-Portal1 Genomics Coordination Center1 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 KircherLab1 BCCM_ULC1 Computational Science at HZDR1 Big data in biomedicine1 TRE-FX1 Guigó lab1 Statistical genetics1 Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation1 Bioinformatics Unit @ CRG1 BSC-CES1 ELIXIR Proteomics1 Black Ochre Data Labs1 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 NIH CFDE Playbook Workflow Partnership1 MMV-Lab1 EMBL-CBA1 EBP-Nor1 Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data1 Bioinformatics Laboratory for Genomics and Biodiversity (LBGB)1 Chemical Data Lab1 Pangenome database project1 HP2NET - Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment1 More...

Independent Teams234 EOSC-Life1 ERGA1

Bart Nijsse13 Jasper Koehorst12 Yvan Le Bras10 Laura Rodriguez-Navas8 Jean-Marie Burel8 Delphine Lariviere6 Coline Royaux5 Sergi Sayols5 Melchior du Lac4 José Mª Fernández4 Bryan Raubenolt4 Juma Bayjan3 Friederike Ehrhart3 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 Andrea Furlani2 Denys Savchenko2 Stian Soiland-Reyes1 Martin Beracochea1 Anne Fouilloux1 Matthias Haimel1 Carlos Oscar Sorzano Sanchez1 Oliver Woolland1 Johannes Köster1 Valentin Tilloy1 Michael Roach1 Elida Schneltzer1 Luiz Gadelha1 Asier Gonzalez-Uriarte1 Woosub Shin1 Ryan Patterson-Cross1 Anthony Bretaudeau1 Haris Zafeiropoulos1 Hrishikesh Dhondge1 Pasi Korhonen1 Marvin Martens1 Tazro Inutano1 Casper de Visser1 Benjamin Wingfield1 Anna Niehues1 Marie-Dominique Devignes1 Samuel Lambert1 Lucas Cruz1 Pablo Riesgo Ferreiro1 Felicita Gernhardt1 Xiaokang Zhang1 Zavolan Lab1 Mahnoor Zulfiqar1 Stevie Pederson1 Veit Schwämmle1 Luiz Gadelha1 Vasiliki Panagi1 Elisabetta Spinazzola1 Agata Kilar1 Akshay Akshay1 Phuong Doan1 Davide Gurnari1 David Yuan1 Justin Sonneck1 Zafran Hussain Shah1 Michael Hall1 Rafael Terra1 Dominik Lux1 Andrii Neronov1 More...

Workflows in EuroScienceGateway10 IDR6 CEITEC CryoEM Facility Workflows3 TronFlow2 Vertebrate Genomes Pipelines (VGP) workflows2

Bioinformatics17 Biodiversity8 Ecology8 Biomedical science6 Genetic variation6 Metagenomics6 Biological databases4 Sequence analysis4 Bioimaging3 Compound libraries and screening3 Drug discovery3 Imaging3 Metagenomic sequencing3 Oncology3 Preclinical and clinical studies3 Protein interactions3 Sample collections3 Sequence assembly3 Data integration and warehousing2 Data mining2 Data quality management2 Genomics2 Protein interaction experiment2 Proteomics2 Quantitative genetics2 Rare diseases2 Sequencing2 Virology2 Workflows2 ChIP-seq1 Computer science1 Data submission, annotation and curation1 DNA polymorphism1 Environmental science1 Epigenomics1 Gene expression1 Gene structure1 Gene transcripts1 Genetics1 Human genetics1 Machine learning1 Medical imaging1 Medical informatics1 Metabolomics1 Metatranscriptomics1 Molecular genetics1 Molecular interactions, pathways and networks1 Ontology and terminology1 Phylogenetics1 Physics1 Protein folds and structural domains1 Protein variants1 Transcriptomics1 More...

Variant calling6 Annotation3 Data retrieval3 Protein interaction network analysis3 Sequence assembly3 Sequencing quality control3 Variant classification3 Variant filtering3 Gene-set enrichment analysis2 Haplotype mapping2 Modelling and simulation2 Prediction and recognition2 Protein interaction network prediction2 SNP annotation2 Analysis1 Calculation1 Clustering1 Conversion1 Correlation1 Data handling1 Dimensionality reduction1 DNA barcoding1 Enrichment analysis1 Expression correlation analysis1 Format detection1 Genome assembly1 ID mapping1 Image analysis1 Metabolic pathway prediction1 Named-entity and concept recognition1 Network analysis1 Peptide identification1 Protein identification1 Protein-protein interaction analysis1 Relation extraction1 RNA-Seq analysis1 Sequence contamination filtering1 Taxonomic classification1 Text annotation1 Text mining1 Transcription factor binding site prediction1 Weighted correlation network analysis1 More...

Stable110 Work-in-progress48 Deprecated2

Passing2