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uniformly preprocess macroscopic gene set by default #56

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qinqian opened this issue Feb 6, 2023 · 0 comments · Fixed by #92
Closed

uniformly preprocess macroscopic gene set by default #56

qinqian opened this issue Feb 6, 2023 · 0 comments · Fixed by #92
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@cameronraysmith @qinqian
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performance Performance python Pull requests that update Python code
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0.1.2

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qinqian commented Feb 6, 2023 •
edited by cameronraysmith
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We want to analyze the PBMC data set with default settings of up to 2000 highly variable genes rather than the top 3 dynamical genes.

I added pipeline stages for pbmc68k and model 2 training with up to 2000 highly variable genes and collected metrics using the dvc pipeline.
@qinqian qinqian self-assigned this Feb 6, 2023
@qinqian qinqian added the performance Performance label Feb 6, 2023
@cameronraysmith cameronraysmith changed the title PBMC data test with default top variable gene selection analyze PBMC data set with default gene selection Feb 6, 2023
@cameronraysmith cameronraysmith added the python Pull requests that update Python code label Feb 6, 2023
@cameronraysmith cameronraysmith added this to the model milestone Feb 13, 2023
@cameronraysmith cameronraysmith modified the milestones: model, 0.1.2 Mar 29, 2023
@cameronraysmith cameronraysmith self-assigned this Mar 30, 2023
@cameronraysmith cameronraysmith changed the title analyze PBMC data set with default gene selection uniformly preprocess macroscopic gene set by default Mar 30, 2023
@cameronraysmith cameronraysmith mentioned this issue Mar 30, 2023
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set preprocessing to macroscopic gene set by default and retrain cameronraysmith/pyrovelocity
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