TCGA HDF file pipeline

HDF files containing data from The Cancer Genome Atlas (TCGA).

https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga

Please see the Broad Institute's TCGA data usage policy: https://broadinstitute.atlassian.net/wiki/spaces/GDAC/pages/844333156/Data+Usage+Policy

The HDF files were generated by the code in this repository: https://github.com/dpmerrell/tcga-pipeline

* tcga_omic.tar.gz contains multi-omic data for 11,000+ patients, divided into 38 cancer types. This includes copy number variation, methylation, gene expression, and RPPA data.

* tcga_clinical.tar.gz contains clinical annotations for those same patients. E.g., age, sex, survival, smoking.

See https://github.com/dpmerrell/tcga-pipeline/blob/main/README.md for more information.

Version notes:

2021-02-28: improved HDF file format. We provide one big matrix of data, rather than one matrix per cancer type. Cancer type is indicated by a vector (key="cancer_types"). Updated the Omic and Clinical HDFs accordingly.

2021-02-01: added mutation annotation scores. removed GRSN from RPPA pipeline.

2021-01-24: removed redundant/combination datasets (COADREAD, STES, GBMLGG, KIPAN). Applied Global Rank-Invariant Set normalization (GRSN) to RPPA data.