cell_ranger HVG flavor inconsistent with 10x code
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Description
It appears that in the cell ranger code, the dispersion is calculated using the negative binomial relationship between mean and dispersion, see
Furthermore, these summary statistics are calculated on the count matrix normalized by library size, but not log-transformed.
As a follow-up, the "Seurat" flavor seems to be no longer used in Seurat. Any plans to implement their "vst" method?
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Research direction
Compare the referenced cellranger stats.py and pca.py implementations, then trace Scanpy's current highly-variable-gene implementation and its existing flavor tests. Define the desired Cell Ranger-compatible normalization and dispersion behavior, and consider the requested Seurat vst method; done means the selected flavor matches the intended method and tests cover its results.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100