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PNNL-CompBio / coderdata

Automation scripts and benchmark dataset package for cancer drug prediction deep learning models.
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Missing 'improve_sample_id' for some cell-lines #10

Closed priyanka9991 closed 1 year ago

priyanka9991 commented 1 year ago

When trying to map DepMap ID to RRID for the CCLE Multiomics data, I found some cell-lines with missing RRID. Then I used the 'samples.csv' file in this folder: candleDataProcessing/data/ to map the DepMap ID to 'improve_sample_id' for those cell-lines with missing RRIDs. However, there are still some cell lines with no improve id as well. I am attaching a list of cell-lines with no RRID and no 'improve_sample_id'. missing_rrid_imp_id

sgosline commented 1 year ago

I haven't added cell lines that aren't in cellosaurus or the data/DepMap_Argonne_Mapping.csv in this repo. If you can send me the mapping information for these cell lines i can add them.

sgosline commented 1 year ago

Update - i'm also using the Model.csv file from depmap, should be using the sample_info.csv file.