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JackieHanLab / TOSICA

Transformer for One-Stop Interpretable Cell-type Annotation
MIT License
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Sharing code to reproduce manuscript figures #2

Closed mariemoullet closed 1 year ago

mariemoullet commented 1 year ago

Hello! This is a super interesting method, I was wondering if you were planning on releasing the code used to generate the figures in the manuscript, or update the tutorial to show how to pull out population-specific pathways (eg Fig4)? Thank you so much for your help!

JackieHanLab commented 1 year ago

Thanks for your appreciation, we may release supplementary code to reproduce all the analyses presented in the TOSICA paper in the future. For now, we have summarized the codes for fig4 in reproducibility, which include how we choose those pathways. Actually, we just used scanpy.tl.rank_genes_groups(method='wilcoxon') to find population-specific pathways and Spearman/Pearson correlation coefficient to find pathways associated with continuous variables. Hope the answer can help you!