Comments (2)
Hi Sarah,
thanks for the note and sorry about that; would you install a stable release from PyPi in the meanwhile pip install scanpy
? I'm currently rewriting quite substantial parts and yes, this is clearly a bug I caused on the weekend; testing will also be more extensive in the future so that this stuff does happen anymore. This kind of stuff will also not happen on master branch in the future; but this rewriting goes along with building some documentation and this builds from master...
Cheers,
Alex
from scanpy.
Could you pull the current version (0.2.7) from github or install it via pip? Everything should be back to normal now.
from scanpy.
Related Issues (20)
- Test full dask support for `log1p`, `normalize_per_cell`, `filter_cells`/`filter_genes`
- Incorrect number setting ofr highly_variable_genes HOT 8
- error in sc.tl.rank_genes_groups HOT 6
- Something wrong with read_10x_mtx using anndata-0.10.4 HOT 1
- Returning/changing genes as upper case instead of capitalized after running rank_genes_groups
- Seeming incompatibility with the numpy matrix subclass HOT 2
- read_10x_mtx() with annData 0.10.4 only reads one variable HOT 1
- 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 2
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