scanpy
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scverse
Single-cell analysis in Python. Scales to >1M cells.
- [x] I have checked that this issue has not already been reported. - [ ] I have confirmed this bug exists on the latest version of scanpy. - [...
- [x] Additional function parameters / changed functionality / changed defaults? - [ ] New analysis tool: A simple analysis tool you have been using and are missing in `sc.tools`?...
Dear, Is there a function that returns mean expression and percentage of each gene in a cluster ? scanpy.api.pl.dotplot() includes these information implicitly, so perhaps it's the easiest way to...
- [X] I have checked that this issue has not already been reported. - [X] I have confirmed this bug exists on the latest version of scanpy. - [X] (optional)...
As we are refactoring scvi, I'm wondering what the utility would be to spin off the i/o part of scanpy into it's own lightweight package that's more general for reading...
In several Scanpy functions `sanitize_anndata()` is called which converts most string columns in `obs`/`var` to categorical columns. Often this seems to be a precaution rather than really necessary and as...
- [x ] I have checked that this issue has not already been reported. - [ x] I have confirmed this bug exists on the latest version of scanpy. -...
- [x] I have checked that this issue has not already been reported. - [] I have confirmed this bug exists on the latest version of scanpy. - [] (optional)...
It would be nice to have a way to split the violin plots from `sc.pl.violin()` into a specific number of rows, similar to the `ncols` parameter in `scanpy.pl.umap()`
Hi! I've noticed that the function `rank_genes_groups` calculate logFC differently than seurat. https://github.com/theislab/scanpy/blob/5800db45dde0c2060ad0a9bed8ea931bd41da936/scanpy/tools/_rank_genes_groups.py#L207-L208 https://github.com/theislab/scanpy/blob/5800db45dde0c2060ad0a9bed8ea931bd41da936/scanpy/tools/_rank_genes_groups.py#L223 Thus the equation is `log(exp(mean(values))` while in Seurat is https://github.com/satijalab/seurat/blob/96d07d80bc4b6513b93e9c10d8a9d57ae7016f9f/R/differential_expression.R#L175-L179 thus `log(mean(exp(values)))` I was thus wondering...
