Workflows
What is a Workflow?Filters
Query
Created At
Updated At
Tool
FastQC40
MultiQC30
anndata23
SAMtools23
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
Falco5
FASTX-Toolkit5
FeatureCounts5
Flye5
gffcompare5
RSeQC5
SRA Software Toolkit5
Unicycler5
annotatemyids4
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...
Workflow type
Galaxy400
Tag
GTN386
Galaxy385
Transcriptomics32
Proteomics28
Ecology23
microbiome22
variant-analysis17
Assembly16
genome-annotation16
Statistics15
Name:neoantigen14
epigenetics12
imaging12
Name:microgalaxy12
Introduction11
name:single-cell11
Computational-chemistry10
Metagenomics10
Name:clinicalmp10
Name:singlecell10
single-cell10
Lg-wf9
Ml9
name:training9
Galaxy-interface8
Name:transcriptomics8
Sequence-analysis7
Amplicon6
Climate6
Metabolomics6
Mgnify_amplicon6
evolution5
name:Collection5
Name:iwc5
Name:pathogfair5
Ocean5
Visualisation5
Earth-system4
Flexynesis4
Machine_learning4
Name:deconv-eval4
Name:scrna-seq4
BY-COVID3
Cheminformatics3
covid-193
hCNV3
Microgalaxy3
Name:by-covid3
Name:seurat3
Name:trajectory_analysis3
pangeo3
synthetic-biology3
textcleaning3
4culture2
bioimaging2
Braker32
BUSCO2
CellProfiler2
Classification2
Contributing2
culturedata2
Deep_learning2
Digitalhumanities2
Ecoregionalization2
FAIR workflows2
GC-MS2
Genomeannotation2
Genomics2
Gleam2
hla2
Humanities2
Iedb2
illumina2
Image_learner2
imageanaylsis2
Jbrowse2
Marineomics2
MIRACUM2
openrefine2
pool_amplicon2
scATAC-seq2
Segmentation2
tabulardata2
vgp2
yolo2
10X1
AI1
Alternative splicing1
alternative-splicing1
annotation pipeline1
Argo1
Asaim1
Audio1
Augustus1
Beacon1
bgc1
Big-data1
binning1
Biodiversity1
Bioimage1
cancer1
Chinese-language1
Chowell_train_test1
Clustering1
CNVkit1
Comparison1
copernicus1
Cut&run1
DE_NOVO1
Deeplearning1
denovo1
Dh1
Diff1
Electrophoresis_gel1
Environmental monitoring1
eukaryotic genome1
Exposomics1
Expospomics1
Fnn1
Formulaassignment1
Fungi1
gene prediction1
Gene_expression1
GeneMark-ET1
Geosciences1
Gtex1
Habitat fragmentation1
Ham100001
Helixer1
IDR1
Image_classification1
Imagerecognition1
Introductions1
isoform switching1
Iwtomics1
Land cover classification1
Landscape ecology1
Linguistics1
Llr6_model1
Logistic_regression_model1
Loris1
Lotus21
Ludwig1
Machine Learning1
map_to_reference1
Marinebiodiversity1
Metaplasmidome1
Mfa1
Mito-flash1
Mitochondrion_tracking1
Mnist1
Moleculardynamics1
Multi-omics1
Multimodal1
Name:bacsnp1
Name:baculoviridae1
Name:baculovirus1
Name:band_intensity1
Name:bioimaging1
Name:brightfieldmicroscopy1
Name:circos1
Name:colordeconvolution1
Name:data-management1
Name:deconvolution1
name:ERGA1
Name:fairymags1
Name:gtn1
Name:histology1
Name:histologystaining1
Name:immunohistochemistry1
Name:massontrichrome1
Name:naldv1
Name:nanopore1
Name:qupath1
Name:scanpy1
Name:sequenceanalysis1
Name:single_cell1
Name:viz1
NFDI4BIOIMAGE1
Noiseestimation1
OMERO1
pathogen1
Phonetics1
Plant1
protein evidence1
Pseudobulk1
Pubmed1
Pubtator1
QCxMS1
RDM1
Recalibration1
referencegenome1
Regression1
Reviewed1
rna1
rna-seq1
Roi1
Sempi31
Sentinel-21
Skin_lesion1
Smfish1
synthetic data1
Tabpfn1
Text1
Text_mining1
Text-mining1
Tissue_classification1
training1
transcription1
tuberculosis1
Vegetation1
Vegetation index1
VGP_curated1
Video1
visualization1
Voronoi1
Whisper1
workflow1
More...
Submitter
GTN Bot384
Helena Rasche4
Cristóbal Gallardo3
Khaled Jum'ah2
Pauline Seguineau2
Molène Mahé2
Bert Droesbeke1
Saskia Hiltemann1
Daniela Schneider1
More...
Team
Galaxy Training Network400
EuroScienceGateway18
BY-COVID (general)2
Space
Galaxy400
ELIXIR20
Creator
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...
Collection
Workflows in EuroScienceGateway18
BY-COVID related workflows2
Biodiversity & ecology workflows1
Topic annotations
Ecology3
Copy number variation2
Transcriptomics2
Biodiversity1
Biomedical science1
Data visualisation1
Genetic variation1
Microbiology1
More...
Operation annotations
Copy number variation detection2
Visualisation2
Antimicrobial resistance prediction1
Copy number estimation1
Data filtering1
Data sorting1
Gene prediction1
Genetic mapping1
Genome annotation1
Read mapping1
Sequence alignment1
Sequence assembly1
Sequencing quality control1
Structural variation detection1
Text mining1
Transcriptome assembly1
More...
Scientific disciplines
Computer Science395
Maturity
Stable25
Work-in-progress3
400
Workflows visible to you, out of a total of 400
Tutorial explaining how to use the Montreal Forced Aligner (MFA)
Associated Tutorial
This workflows is part of the tutorial Montreal Forced Aligner, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Train an Image Learner tissue classifier from prepared GTEx v11 expression images and metadata.
Associated Tutorial
This workflows is part of the tutorial GTEx Tissue Modeling with Galaxy Image Learner, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
This is the workflow for the Batch Correction and Integration tutorial if you use Seurat.
Associated Tutorial
This workflows is part of the tutorial Batch Correction and Integration with Seurat or Scanpy, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Workflow for GTN tutorial on single-cell batch correction, using the Scanpy pipeline with Harmony.
Associated Tutorial
This workflows is part of the tutorial Batch Correction and Integration with Seurat or Scanpy, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
This workflow performs colour deconvolution and automated thresholding to quantify stained area in brightfield histological images (MT, IHC). It accepts whole slides or pre-cropped ROIs.
Associated Tutorial
This workflows is part of the tutorial Quantitative Analysis of Histological Staining Using Color Deconvolution, available in the GTN ...
Metaproteomics 101 tutorial
Associated Tutorial
This workflows is part of the tutorial Metaproteomics tutorial, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
This WF applies Flexynesis on BRCA data from Metabric for a classification task
Associated Tutorial
This workflows is part of the tutorial Modeling Breast Cancer Subtypes with Flexynesis, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Regression in Machine Learning
Associated Tutorial
This workflows is part of the tutorial Regression in Machine Learning, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
22_04_30: WF Update
The workflow serves as a short introduction to Galaxy for users from the Humanities who mostly work with texts.
Associated Tutorial
This workflows is part of the tutorial Introduction to Digital Humanities in Galaxy, available in the GTN
Features
- Includes [Galaxy Workflow ...
Workflow used for the Ecology tutorial devoted to use yolo model on SEANOE marine data
Associated Tutorial
This workflows is part of the tutorial Object detection with YOLO, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a ...
