Explore Workflows

Motif Finding with HOMER with custom background regions --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

https://github.com/datirium/workflows.git

Path: workflows/homer-motif-analysis-bg.cwl

Branch/Commit ID: 104059e07a2964673e21d371763e33c0afeb2d03

ChIP-seq 02 trimming - reads: PE

https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/02-trim-pe.cwl

Branch/Commit ID: 1a0dd34d59ec983d1f7ad77bff35da2f016e3134

ChIP-seq 01 QC - reads: PE

https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/01-qc-pe.cwl

Branch/Commit ID: 1a0dd34d59ec983d1f7ad77bff35da2f016e3134

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: 2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71

ChIP-seq 03 mapping - reads: PE

https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/03-map-pe.cwl

Branch/Commit ID: 1a0dd34d59ec983d1f7ad77bff35da2f016e3134

ChIP-seq - Quantification - samples: treatment

https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/05-quantification.cwl

Branch/Commit ID: 1a0dd34d59ec983d1f7ad77bff35da2f016e3134

https://github.com/hubmapconsortium/sprm.git

Path: pipeline.cwl

Branch/Commit ID: 99d30aacfba3c2c9a9acd0fe4472120c56bd32a4

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f

https://github.com/reanahub/reana-demo-worldpopulation.git

Path: workflow/cwl/worldpopulation-htcondorcern.cwl

Branch/Commit ID: b5cbebcc97f2c71396203257ba98deb01de59697

https://github.com/litd/analysis-workflows.git

Path: definitions/subworkflows/strelka_process_vcf.cwl

Branch/Commit ID: 336f7d1af649f42543baa6be2594cd872919b5b5