Explore Workflows

https://git.astron.nl/RD/LINC.git

Path: workflows/LBA_calibrator.cwl

Branch/Commit ID: ee2e8e751a5202b670d6543d932757c00fb3bb03

Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file.

https://github.com/Barski-lab/workflows.git

Path: workflows/rnaseq-pe-dutp.cwl

Branch/Commit ID: 0d919fc3a2f4e4c105142df04d74ac934e3c8c03

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

Path: cwltool/schemas/v1.0/v1.0/dynresreq-workflow.cwl

Branch/Commit ID: aaaece1c097c3f06afa21f7ecddcc85519e2bb2b

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: 57437c1e9f881411b65f79acd64b7cf14df5b901

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines9-wf-noET.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

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

Path: testdata/step_valuefrom5_wf_with_id_v1_2.cwl

Branch/Commit ID: 15c8467d6d3c31a95ccc682095cf34aad125ca8c

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

Path: testdata/workflow_input_format_expr_v1_2.cwl

Branch/Commit ID: 15c8467d6d3c31a95ccc682095cf34aad125ca8c

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

Path: testdata/count-lines7-single-source-wf_v1_2.cwl

Branch/Commit ID: 15c8467d6d3c31a95ccc682095cf34aad125ca8c

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

Path: testdata/workflow_input_format_expr_v1_1.cwl

Branch/Commit ID: 15c8467d6d3c31a95ccc682095cf34aad125ca8c

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

Path: testdata/step-valuefrom3-wf_v1_1.cwl

Branch/Commit ID: 15c8467d6d3c31a95ccc682095cf34aad125ca8c