Additional functionality
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- Python
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Description
Dear all, I'm currently using scanpy exhaustively and have noticed that compared to other R scRNA-seq packages some nice functionality is still missing.
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Scater has the plotExplanatoryVariables function which plots the variance explained by different features (https://rdrr.io/bioc/scater/man/plotExplanatoryVariables.html). Is there currently an alternative in Scanpy for this plot?
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Is there a variant for the mvoutlier package that is proposed in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408845/ for cell filtering?
Kind regards
Dries De Maeyer
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 reviewing the linked Scater plotExplanatoryVariables documentation and the mvoutlier paper, then determine whether Scanpy already provides alternatives for either request. The work is done when the requested plotting and cell-filtering functionality has a defined scope, implementation, and corresponding validation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data-visualization
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100