Comments (4)
That’s strange, because I made this change to fix this in some situations.
-gex_rows = [x == "Gene Expression" for x in adata.var["feature_types"]]
+gex_rows = adata.var["feature_types"] == "Gene Expression"
return adata[:, gex_rows].copy()
Seems like this function needs even more work.
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Hi I encountered the same issue. It cannot read mtx and features appropriately.
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I have the same problem. Didn't expect it is due to the anndata package.
Downgrade anndata to 0.10.2 solve this problem.
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OK, this is indeed fixed in scanpy master and the bugfix branch (1.9.x). Please try installing the current bugfix branch:
pip install 'scanpy @ git+https://github.com/scverse/[email protected]'
We will release a new feature version in 3 weeks, so there will probably be no bugfix release before that.
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Related Issues (20)
- Unify `method`/`flavor`/`backend`/… parameters
- Parameter docs render text in backticks as `<cite/>` text HOT 1
- Unable to plot embedding after Scanpy release 1.9.7 HOT 4
- pytest 8 compatibility HOT 2
- Fix plotting warnings raised in tutorial notebooks HOT 2
- Violin plots in Preprocessing and clustering 3k PBMCs tutorial HOT 4
- Documentation for percent_top= in scanpy.pp.calculate_qc_metrics is unclear and contradictory HOT 4
- Use of fast_matrix_market library to read mtx files HOT 1
- ValueError: b'Extrapolation not allowed with blending' when using `"sc.pp.highly_variable_genes"` function HOT 3
- sc.pp.subsample, allow for sampling with replacement HOT 1
- String conversion of `qc_vars` into a `Collection` when a `str` input is provided in `calculate_qc_metrics`
- ``biomart_annotations`` still creates cache when ``use_cache=False`` HOT 2
- Submodular optimization using apricot HOT 3
- Change default leiden clustering backend to `igraph`, and reduce default number of iterations HOT 6
- Scanorama causing segfault on CI HOT 1
- Rename master -> main HOT 4
- More in depth example for `neighbors(transformer=...)` HOT 1
- scanpy 1.10.0rc1 breaks anndata pre-release tests
- log1p return matrix HOT 1
- Leiden and louvain params not saved to matching `key_added` key in `uns` dictionary
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