Could data from UCSC Xena used as an input for PyDESeq2?
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Description
Hi, thanks for your great job.
I am going to do DEA based on data downloaded from UCSC Xena:
I wonder if PyDESeq2 could deal with these data (e.g. RSEM expected_count (DESeq2 standardized)). Is 'raw read count' strictly needed as an input for PyDESeq2?
Thanks in advance and really looking forward to hearing from you.
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Research direction
The issue names no file, test, or entry point. Begin with PyDESeq2's documented input requirements and compare them with UCSC Xena RSEM expected_count data; done would clearly state whether this input is supported and, if not, define the required support or conversion guidance.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100