scanpy
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Single-cell analysis in Python. Scales to >1M cells.
- [ 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. -...
In `sc.pp.highly_variable_genes()` when `flavor='cell_ranger'` and `n_top_genes` is set check that enough normalized dispersions have been calculated and if not raise a warning and set `n_top_genes` to the number of calculated...
Fixes #2246 A very small change with a small test. The new test fails for the current master branch, but passes with the fix.
Hi there, using `sc.read(filename, ext='txt')` I get the following irrelevant warning: `WARNING: Your filename has more than two extensions: ['.5_E9', '.0_E9', '.5', '.txt']. Only considering the two last: ['.5', '.txt']....
- [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)...
When I use `sc.pp.log1p(adata)` and then `sc.pp.log1p(adata, layer='other')` it warns me that the data has already been logged even though I am logging a layer as opposed to adata.X. Would...
Hey there, Found out today (from [a question on discourse](https://discourse.scverse.org/t/add-title-to-scanpy-pl-heatmap/644)) that some plotting documentation is misleading. The ['return' section](https://github.com/scverse/scanpy/blob/41a7b830acb0c05ca4cbf0bea97e3fa17545f12c/scanpy/plotting/_anndata.py#L1009) for `heatmap`, `tracksplot` and potentially other functions as well should be...
- [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. - [ ]...
This PR aims to add more GPU functionalities and to integrate more an exisiting one: * `tl.draw_graph` and `tl.leiden` can now both be GPU accelerated using rapids framework. * on...
This is a bit of a catch all to improve cite-seq support. Currently a dependency of https://github.com/theislab/scanpy-tutorials/pull/14. I'll write a bit more about this after some sleep. The main goals...
