hweej/datahub-study-curation-tools

Contains tools used by cBioPortal data curators when preparing data for upload into the datahub repos.

Introduction

Data curation scripts for cBioPortal. Curated data sets can be found in Datahub.

Directory layout

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├── archive                         # legacy tools 
├── GN-annotation-wrapper           # MAF genome-nexus annotation 
├── add-clinical-header             # attach header lines to clinical files  
├── gene-table-update               # tools for updating seedDB gene tables  
├── generate-case-lists             # generate case lists  
├── hugo-symbol-corrector           # correct hugo symbols convereted to dates by Microsoft Excel 
├── TMB                             # tumor mutation burden calculation
├── validation                      # validator wrapper and tools for validator 
├── oncotree-code-converter         # add `cancer_type` and `cancer_type_detailed` based on oncotree code
├── map-ids                         # rewrite IDs used in a study sample/patient ID maps
├── subset-data                     # subset study based on sample/patient ID list
├── zscores                         # calculate z-scores
├── LICENSE  
└── README.md