grunwaldlab / grunwaldlab/metacoder
Using ANCOM-BC2 for DA analysis
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- Dominant language
- R
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- 148
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- 30
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Description
Hello,
After benchmark testing of different DA methods for my dataset, I discovered that DESeq2 with poscounts and ANCOM-BC2 are the most performant tests for DA analysis. Thus, I was wandering is it somehow possible to use DESeq2 with poscounts estimation or ANCOM-BC2 as DA test?
Thank you for your cooperation,
Ivan
Contributor guide
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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
No files, tests, or entry points are named. Start by locating the existing differential-abundance test integration and reviewing how DESeq2 options are configured; done means establishing whether DESeq2 with poscounts and ANCOM-BC2 are supported, with tests covering the selected methods.
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Assessment
- Tech stack
- r
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100