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emdann / sc_target_evidence

Meta-analysis of drug target evidence in single-cell data
BSD 3-Clause "New" or "Revised" License
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How to obtain the original unaggregated cxg dataset #14

Closed mrbeann closed 4 months ago

mrbeann commented 4 months ago

Thanks for this amazing work. I was wondering how can I get the original cxg dataset. I try to use the "sc_target_evidence/src/process_sc_data.py", but it seems "TargetDiseasePairs_OpenTargets_cellXgeneID_12072023.csv" is missing.

emdann commented 4 months ago

Hi @mrbeann, thanks for pointing this out! In practice you only need that file if you set --keep_all_genes to False in the script parameters (which we never did in the final analysis). That table contains the list of gene-disease pairs included in Open Targets, which are included in the results table.

I will amend the scripts to avoid future confusion during revision.

mrbeann commented 4 months ago

Thank you for your reply. But the format in "suppl_table_disease_target_evidence.csv" seems different from "TargetDiseasePairs_OpenTargets_cellXgeneID_12072023.csv", and this file will read even if --keep_all_genes to True. I guess you mean we can skip Line 61 "all_genes_ls.extend(target_genes)"?