/TCGA-Level-3

Integrative analysis of Level 3 TCGA Data (e.g. gene/exon quant)

Primary LanguagePythonMIT LicenseMIT

Level 3 TCGA Data Tools

This project is for working on tools for munging/analyzing TCGA Level 3 data, along with the cwl.json files for use on the Seven Bridges Cancer Genomics Cloud.

gene_expression_munger

This tool integrates RNAseq gene expression data (raw counts) into a clean matrix. When used on the Seven Bridges Cancer Genomics Cloud, it also produced a matrix of metadata attributes for each case analyzed.

To test locally: python gene_expression_munger.py -f Gene_Exp_Test/* -c

For testing the use of an index file: python gene_expression_munger.py -r Gene_Exp_Test/test.index -c