Scripts-RNA-Pathway-Analysis

Scripts for RNA clean-up, exploratory data analysis, and pathway analysis

Merging and clean-up

Example for many Uses re-formatted CCLE example for demonstration; used for compiling across samples.

Pathway analysis with GSVA

Running Gene Set Variation Analysis (GSVA) on expresson data for a set of samples using the MSIGDB Cancer Hallmarks

Heatmap of GSVA results

Using package ComplexHeatmap to create a nice heatmap output for GSVA enrichment scores. Optional: add annotation to samples alongside of heatmap, see R markdon.