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Graph	Name	Retrieved From	View
	Motif Finding with HOMER with random background regions 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: c6bfa0de917efb536dd385624fc7702e6748e61d
	count-lines5-wf.cwl	https://github.com/common-workflow-language/cwl-v1.1.git Path: tests/count-lines5-wf.cwl Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
	Run pindel on provided region	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/pindel_region.cwl Branch/Commit ID: f42c889734c8f709ad2fd9090493bcaac8326c98
	Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/pvacseq.cwl Branch/Commit ID: 735be84cdea041fcc8bd8cbe5728b29ca3586a21
	Single-cell ATAC-Seq Cluster Analysis Single-cell ATAC-Seq Cluster Analysis Clusters single-cell ATAC-Seq datasets, identifies differentially accessible peaks.	https://github.com/datirium/workflows.git Path: workflows/sc-atac-cluster.cwl Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf
	Cell Ranger Aggregate Cell Ranger Aggregate Aggregates outputs from multiple runs of Cell Ranger Count Gene Expression or Cell Ranger Multi Gene Expression and V(D)J Repertoire Profiling experiments	https://github.com/datirium/workflows.git Path: workflows/cellranger-aggr.cwl Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e
	trim-chipseq-pe.cwl Runs ChIP-Seq BioWardrobe basic analysis with paired-end input data files.	https://github.com/Barski-lab/workflows.git Path: workflows/trim-chipseq-pe.cwl Branch/Commit ID: ca2dbb71d0537b1d93a8bd44719250cf8949b157
	sum-wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/sum-wf.cwl Branch/Commit ID: 75271e2a0887d47cca4077b60dd51ac763c09b63
	Deprecated. Single-Cell Preprocessing Pipeline Devel version of Single-Cell Preprocessing Pipeline ===================================================	https://github.com/datirium/workflows.git Path: workflows/single-cell-preprocess.cwl Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869
	revsort.cwl Reverse the lines in a document, then sort those lines.	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/revsort.cwl Branch/Commit ID: 886a6ac41c685f20d39e352f9c657e59f3312265