TCGA_survival_analysis

Description

A workflow for survival analysis of cancer patients from the Cancer Genome Atlas project. This survival analysis is based off of mRNA expression levels. This workflow is a modified implementation of a similar procedure described on biostars.org: https://www.biostars.org/p/153013/

The workflow is contained in the survival_analysis.ipynb jupyter notebook.

Requirements

Programming languages

• Python 3.6.7
• R 3.6.0

(language versions are probably flexible)

Python packages

• Pandas
• rpy2
• Numpy
• glob

R libraries

• DESeq2
• survival
• survminer