Use ChipSeekR to visualise DMRs

Epigenomics-Screw / Screw

SCREW: A Reproducible Workflow for Single-Cell Epigenomics

MIT License

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Use ChipSeekR to visualise DMRs #37

Open oneillkza opened 6 years ago

oneillkza commented 6 years ago

Description

As a bioinformatician, I would like to display the regions DMRs fall within, and annotate them to genes.

Estimate

Priority

SHOULD

Notes

input should be:
- A BED file specifying regions of interest (for testing purposes I've added an example bed file to the test_metadata)
- A string specifying the genome (for testing purposes use 'hg19')
output should be an Rmd document

http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html

oneillkza commented 6 years ago

@jjonphl this would be a useful small unit of coding for you to work on. @cmorganl and @sibylgisela have been putting together code for rendering/generating Rmd documents within CWL, so hit them up for some advice on that. But the first step would be putting together an Rmd.