DepMap Data Curation

[Rima-Waleed]

Publication: https://www.nature.com/articles/s41586-019-1186-3 Data source: https://depmap.org/portal/download/all/

Please keep this checklist for curation of a new study.

• [ ] create an issue on datahub before curating a study (one issue per study) and copy this checklist to the issue tracker
• [ ] List information of the dataset/paper in the issue, e.g. pmid, paper link, suppl file link
• [ ] Document the curation process, e.g. how and by whom the data was transformed
• [ ] Follow the data checklist
• [ ] Create a pull request to datahub once the data is curated
• [ ] Push to triage portal
• [ ] Import into msk and public portal database
• [ ] Update the default quick select study list see https://github.com/cBioPortal/cbioportal/issues/5831 (only for studies that are not overlapping with existing ones; only for human tumors, not cell lines)
• [ ] Update cBioPortal news

[Rima-Waleed]

• [x] Model.csv —> data_clinical_patient
• [x] Model.csv —> data_clinical_sample
• [x] OmicsCNSegmentsProfile.csv —> data_cna_hg38.seg
• [x] OmicsSomaticMutationsMAFProfile—> data_mutations
• [x] OmicsFusionFiltered.csv —> data_sv
• [x] OmicsExpressionProteinCodingGenesTPMLogp1 —> data_RNA_Seq_v2_expression_median & data_RNA_Seq_v2_expression_median_zscores
• [x] OmicsCNGene.csv —> data_log2_cna