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Teichlab / bbknn

Batch balanced KNN
MIT License
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kernals died when using bbknn #60

Closed FessenSimon closed 1 month ago

FessenSimon commented 1 month ago

I'm trying to do bbknn with my own single-cell data and demo data, but kernals died every time when I doing whatever my own data or demo data. Is this because of my device? or?

sc.settings.verbosity = 3sc.logging.print_header() sc.settings.set_figure_params(dpi=80) scanpy==1.10.1 anndata==0.10.5.post1 umap==0.5.5 numpy==1.26.4 scipy==1.11.1 pandas==2.2.2 scikit-learn==1.3.0 statsmodels==0.14.0 igraph==0.11.5 louvain==0.8.2 pynndescent==0.5.11

adata = sc.read('pancreas.h5ad', backup_url='https://www.dropbox.com/s/qj1jlm9w10wmt0u/pancreas.h5ad?dl=1') bbknn.bbknn(adata, batch_key='batch')

ktpolanski commented 1 month ago

It's almost certainly because of the package annoy. Try running bbknn with computation="cKDTree".

Known ways to try to get annoy to cooperate is creating a fresh conda environment, or installing a different version from pip.

FessenSimon commented 1 month ago

Thank u! Now it's working well!