scanorama corrected matrices
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Description
- Additional function parameters / changed functionality / changed defaults?
- New analysis tool: A simple analysis tool you have been using and are missing in
sc.tools? - New plotting function: A kind of plot you would like to seein
sc.pl? - External tools: Do you know an existing package that should go into
sc.external.*? - Other?
Hi,
"Scanorama outputs both corrected expression matrices and embeddings." However, scanpy.external.pp only implemented .scanorama_integrate #1332 . Is there any plan to implement the .scanorama_correct method as well? Or let .scanorama_integrate output the correct matrices as an option.
Thanks!
Hurley
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 in scanpy.external.pp and compare the existing .scanorama_integrate implementation with issue #1332 and Scanorama's corrected-matrix output. Determine whether completion should add .scanorama_correct or an option on .scanorama_integrate, then verify that the selected API exposes corrected expression matrices as requested.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100