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pinellolab / STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
http://stream.pinellolab.org
GNU Affero General Public License v3.0
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dimension_reduction jupyter kernel dies #143

Open vjbaskar opened 1 year ago

vjbaskar commented 1 year ago

The jupyter kernel dies when I run dimension_reduction function with ~200,000 cells. I am running stream==1.0.0 now. Is there any suggestion on how to run it or if I can skip this step and use the scanpy's dim reductions such as PCA?

Thanks.

huidongchen commented 1 year ago

The jupyter kernel dies when I run dimension_reduction function with ~200,000 cells. I am running stream==1.0.0 now. Is there any suggestion on how to run it or if I can skip this step and use the scanpy's dim reductions such as PCA?

Thanks.

Hi, 200k cells might be too large for the current implemented algorithm. In this case, you have the option to bypass this step by utilizing alternative dimension reduction methods like PCA and saving the result to the field adata.obsm['X_dr'].