Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
|---|---|---|---|
|
|
Feature expression merge - combines feature expression from several experiments
Feature expression merge - combines feature expression from several experiments ========================================================================= Workflows merges RPKM (by default) gene expression from several experiments based on the values from GeneId, Chrom, TxStart, TxEnd and Strand columns (by default). Reported unique columns are renamed based on the experiments names. |
https://github.com/datirium/workflows.git
Path: workflows/feature-merge.cwl Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e |
|
|
|
DiffBind - Differential Binding Analysis of ChIP-Seq or CUTß&RUN/Tag Peak Data
Differential Binding Analysis of ChIP-Seq or CUT&RUN/Tag Peak Data --------------------------------------------------- DiffBind processes ChIP-Seq or CUT&RUN/Tag data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by peak caller tools and aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously, representing different ChIP or CUT&RUN/Tag experiments (antibodies, transcription factor and/or histone marks, experimental conditions, replicates) as well as managing the results of multiple peak callers. For more information please refer to: ------------------------------------- Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin S, Palmieri C, Caldas C, Carroll JS (2012). “Differential oestrogen receptor binding is associated with clinical outcome in breast cancer.” Nature, 481, -4. |
https://github.com/datirium/workflows.git
Path: workflows/diffbind.cwl Branch/Commit ID: bf80c9339d81a78aefb8de661bff998ed86e836e |
|
|
|
count-lines3-wf.cwl
|
https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines3-wf.cwl Branch/Commit ID: 7ec307b01442936fad9b1149f4500496557505ff |
|
|
|
count-lines17-wf.cwl
|
https://github.com/common-workflow-language/cwl-v1.1.git
Path: tests/count-lines17-wf.cwl Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7 |
|
|
|
Cut-n-Run pipeline paired-end
Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed |
https://github.com/datirium/workflows.git
Path: workflows/trim-chipseq-pe-cut-n-run.cwl Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e |
|
|
|
super-enhancer.cwl
Both `islands_file` and `islands_control_file` should be produced by the same cwl tool (iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl) |
https://github.com/Barski-lab/workflows.git
Path: workflows/super-enhancer.cwl Branch/Commit ID: ca2dbb71d0537b1d93a8bd44719250cf8949b157 |
|
|
|
io-int-optional-wf.cwl
|
https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/io-int-optional-wf.cwl Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5 |
|
|
|
Single-cell ATAC-Seq Genome Coverage
Single-cell ATAC-Seq Genome Coverage Creates genome coverage bigWig files from the provided fragments file and selected grouping parameters |
https://github.com/datirium/workflows.git
Path: workflows/sc-atac-coverage.cwl Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e |
|
|
|
metabarcode (gene amplicon) analysis for fastq files
protein - qc, preprocess, annotation, index, abundance |
https://github.com/MG-RAST/pipeline.git
Path: CWL/Workflows/metabarcode-fastq.workflow.cwl Branch/Commit ID: f906212e2c9a88280ae36545e5422f25752aa8f4 |
|
|
|
Cell Ranger Count Gene Expression
Cell Ranger Count Gene Expression ================================= |
https://github.com/datirium/workflows.git
Path: workflows/single-cell-preprocess-cellranger.cwl Branch/Commit ID: cbefc215d8286447620664fb47076ba5d81aa47f |
