Add `scanorama.correct_scanpy` function to `sc.external.pp`
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- Dominant language
- Python
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Description
Currently there's only a wrapper for scanorama.integrate_scanpy
From https://github.com/brianhie/scanorama:
The function integrate_scanpy() will simply add an entry into adata.obsm called 'X_scanorama' for each adata in adatas. obsm['X_scanorama'] contains the low dimensional embeddings as a result of integration, which can be used for KNN graph construction, visualization, and other downstream analysis.
The function correct_scanpy() is a little more involved -- it will create new AnnData objects and replace adata.X with the Scanorama-transformed cell-by-gene matrix, while keeping the other metadata in adata as well.
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 at the existing scanorama.integrate_scanpy wrapper exposed through sc.external.pp and compare it with Scanorama's correct_scanpy behavior. Done means exposing correct_scanpy, creating the transformed cell-by-gene AnnData objects, replacing adata.X, and preserving the other adata metadata described in the issue.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100