Adding LRT test
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- Python
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Description
Hey, thanks for developing pydeseq2!
I used to perform DGE analysis with edgeR and happy now to see there is a python package. I am comparing the result of pydeseq2 and edger on the same dataset and I see there is a large difference. Is it possible to add likelihood ratio test like in deseq2 with dds = DESeq(dds, test="LRT") in the future? Thanks a lot!
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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- Open a pull request that references the issue number.
Research direction
Start by reviewing the requested DESeq(dds, test="LRT") behavior and how PyDESeq2 currently performs differential expression testing. Define the expected LRT results and compare them with DESeq2 and edgeR on equivalent data. Done means LRT is supported with tests covering its statistical output and user-facing behavior.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100