Add alternate shrinkage methodology to deseq2/differential
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Description
Is your feature request related to a problem? Please describe
A single shrinkage method (ashr) is currently hard-coded into deseq2/differential, because I encountered dependency issues with other variants.
Describe the solution you'd like
We should try harder to make alternate shinkage (e.g. apeglm) work. This will likely require updates to the bioconda recipe.
Describe alternatives you've considered
No response
Additional context
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
Start by reading the deseq2/differential module and the bioconda recipe, then review the related nf-core/differentialabundance issue 152. Determine how alternate shrinkage methods such as apeglm can be supported without the dependency problems described; done means an alternate method works and the required recipe updates are included.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100