Alternative implementation using SeSAMe QC, limma for DMPs and DMRcate for DMRs
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Description
Description of feature
I have developed an alternative version of the methylarray pipeline based on a different analytical approach:
SeSAMe for QC (pOOBAH detection p-values)
limma for DMP analysis
DMRcate for DMR calling
Custom filtering of XY/non-CG/bead probes
I would like to propose this as a contribution. Would the maintainers be open to integrating this as an alternative method, or should I submit it as a standalone PR?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
The issue describes an alternative methylation analysis using SeSAMe, limma, DMRcate, and custom probe filtering, but names no files, tests, or entry points. First clarify whether this belongs in the pipeline or a standalone contribution; done is not defined until the integration scope and validation expectations are agreed.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100