Explore Workflows

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

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: adcae308fdccaa1190083616118dfadb4df65dca

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/scatter-wf1_v1_1.cwl

Branch/Commit ID: b926e330eba795f3acc1f71fd0645e75f925a2da

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

Path: tests/wf/816_wf.cwl

Branch/Commit ID: 6b8f06a9f6f6a570142c7aedc767fea2efa2a0cc

Single-Cell ATAC-Seq Dimensionality Reduction Analysis Removes noise and confounding sources of variation by reducing dimensionality of chromatin accessibility data from the outputs of “Single-Cell Multiome ATAC and RNA-Seq Filtering Analysis” pipelines. The results of this workflow are primarily used in “Single-Cell ATAC-Seq Cluster Analysis” or “Single-Cell WNN Cluster Analysis” pipelines.

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

Path: workflows/sc-atac-reduce.cwl

Branch/Commit ID: 57863b6131d8262c5ce864adaf8e4038401e71a2

Cellranger Reanalyze ====================

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

Path: workflows/cellranger-reanalyze.cwl

Branch/Commit ID: 57863b6131d8262c5ce864adaf8e4038401e71a2

https://github.com/umccr/cwl-ica.git

Path: workflows/dragen-germline-pipeline/4.2.4/dragen-germline-pipeline__4.2.4.cwl

Branch/Commit ID: 655acd3c7b6df8c7a54457f70e726c37e69f90bf

https://github.com/umccr/cwl-ica.git

Path: workflows/umccrise-pipeline/2.3.0--0/umccrise-pipeline__2.3.0--0.cwl

Branch/Commit ID: 655acd3c7b6df8c7a54457f70e726c37e69f90bf

Single-Cell WNN Cluster Analysis Clusters cells by similarity on the basis of both gene expression and chromatin accessibility data from the outputs of the “Single-Cell RNA-Seq Dimensionality Reduction Analysis” and “Single-Cell ATAC-Seq Dimensionality Reduction Analysis” pipelines run sequentially. The results of this workflow are used in the “Single-Cell Manual Cell Type Assignment”, “Single-Cell RNA-Seq Differential Expression Analysis”, “Single-Cell RNA-Seq Trajectory Analysis”, “Single-Cell Differential Abundance Analysis”, “Single-Cell ATAC-Seq Differential Accessibility Analysis”, and “Single-Cell ATAC-Seq Genome Coverage” pipelines.

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

Path: workflows/sc-wnn-cluster.cwl

Branch/Commit ID: 57863b6131d8262c5ce864adaf8e4038401e71a2

https://github.com/cr-ste-justine/chujs-alignment-workflow.git

Path: workflows/kfdrc_alignment_wf.cwl

Branch/Commit ID: f2a1a903cfdd8d339e022ef65a55e2d71e8d93b1

Motif Finding with HOMER with random 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. Here is how we generate background for Motifs Analysis ------------------------------------- 1. Take input file with regions in a form of “chr\" “start\" “end\" 2. Sort and remove duplicates from this regions file 3. Extend each region in 20Kb into both directions 4. Merge all overlapped extended regions 5. Subtract not extended regions from the extended ones 6. Randomly distribute not extended regions within the regions that we got as a result of the previous step 7. Get fasta file from these randomly distributed regions (from the previous step). Use it as background 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.cwl

Branch/Commit ID: 57863b6131d8262c5ce864adaf8e4038401e71a2