Plans to add DESeqDataSetFromTximport?
Open
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 761
- Forks
- 90
- Avg merge
- 25m
- Merged PRs (30d)
- 10
Description
Hi,
I was wondering if there is any plans to add a functionality similar to R's DESeqDataSetFromTximport()?
Currently salmon data cannot be used in python unless it is rounded, which is not really the correct way to do it.
Since there now is also a pytximport package I was wondering if something is in the works.
Best
Anne
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 comparing the requested DESeqDataSetFromTximport() functionality with the pytximport package and how PyDESeq2 currently handles salmon data. The work is complete when salmon input can be used in PyDESeq2 without rounding it first, with behavior aligned to the requested R functionality.
Written by the indexing model from the issue text.
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
- 25/100