Auto-generation of Study files for Single Cell Portal submission
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- Dominant language
- Python
- Stars
- 2.6k
- Forks
- 779
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 27
Description
I have recently been using scanpy to analyze my data and get it into a format that I want to share with others. I've been doing that using the Broad's Single Cell Portal, which I suspect others use as well. It took me a couple of hours to figure out the details of file formatting, etc, but I realize the process could be easily automated. Given an adata object, a list of files can be generated that are formatted correctly for upload. I have written this function and I use it myself.
Is scanpy interested in a function that does this? Where in the code would such a thing go?
I'd be happy to create a pull request, but didn't want to go ahead unless there's interest.
Or maybe anndata is a better place for something like this?
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
No files, tests, or entry points are named. Start by reviewing the boundaries between scanpy and anndata and the existing submission-related functionality, then compare the proposed function with the Single Cell Portal's required file formats. Done means an agreed project location and a defined set of correctly formatted files generated from an adata object.
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