Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph Single-cell Multiome ATAC and RNA-Seq Alignment

Single-cell Multiome ATAC and RNA-Seq Alignment Runs Cell Ranger ARC Count to quantifies chromatin accessibility and gene expression from a single-cell Multiome ATAC and RNA-Seq library

 https://github.com/Barski-lab/scRNA-Seq-Analysis.git

Path: workflows/sc-multiome-align-wf.cwl

Branch/Commit ID: 7bbe737324bb6f21f244dea09a926dc2774ed731
workflow graph Single-cell RNA-Seq Aggregate

Single-cell RNA-Seq Aggregate Aggregates gene expression data from multiple Single-cell RNA-Seq Alignment experiments.

 https://github.com/Barski-lab/scRNA-Seq-Analysis.git

Path: workflows/sc-rna-aggregate-wf.cwl

Branch/Commit ID: 7bbe737324bb6f21f244dea09a926dc2774ed731
workflow graph Single-cell Multiome ATAC and RNA-Seq Aggregate

Single-cell Multiome ATAC and RNA-Seq Aggregate Aggregates data from multiple Single-cell Multiome ATAC and RNA-Seq Alignment experiments

 https://github.com/Barski-lab/scRNA-Seq-Analysis.git

Path: workflows/sc-multiome-aggregate-wf.cwl

Branch/Commit ID: 7bbe737324bb6f21f244dea09a926dc2774ed731
workflow graph Single-cell Reference Indices

Single-cell Reference Indices Builds a Cell Ranger and Cell Ranger ARC compatible reference folders from the custom genome FASTA and gene GTF annotation files

 https://github.com/Barski-lab/scRNA-Seq-Analysis.git

Path: workflows/sc-ref-indices-wf.cwl

Branch/Commit ID: 7bbe737324bb6f21f244dea09a926dc2774ed731
workflow graph directory.cwl

Inspect provided directory and return filenames. Generate a new directory and return it (including content).

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/directory.cwl

Branch/Commit ID: 4642316a30a95d4f3d135c18f98477886b160094
workflow graph genomics-workspace-cds.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_genomicsWorkspace/genomics-workspace-cds.cwl

Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2
workflow graph split-bams-by-strand-and-index.cwl

Split reads in a BAM file by strands and index forward and reverse output BAM files

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

Path: v1.0/quant/split-bams-by-strand-and-index.cwl

Branch/Commit ID: 7696e7eb27a9251fba53ef4ccacc84cc8f8b0685
workflow graph Cell Ranger Build Reference Indices

Devel version of Cell Ranger Build Reference Indices pipeline =============================================================

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

Path: workflows/cellranger-mkref.cwl

Branch/Commit ID: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5
workflow graph VIRTUS.SE.cwl

https://github.com/yyoshiaki/VIRTUS2.git

Path: workflow/VIRTUS.SE.cwl

Branch/Commit ID: 96ccb37e04af37474771526cf0d85d3ded2005f7
workflow graph Motif Finding with HOMER with target and background regions from peaks

Motif Finding with HOMER with target and background regions from peaks --------------------------------------------------- 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-peak.cwl

Branch/Commit ID: 92f1a6da9c4f85fb51340b01b32373a50fde0891