HCI011_RNAseq

This repository contains the data and code for the RNA-seq analysis done in the paper FOXM1 is a biomarker of resistance to PI3Kα inhibition in ER+ breast cancer that is detectable using metabolic imaging (Ros et al. 2020).

Input data includes processed gene counts and sample metadata information, and the gene lists used in the analysis.

Requirements

R (>= 3.61) with these packages:

• plyr
• dplyr
• tibble
• data.table
• RColorBrewer
• pheatmap
• svglite (only required if wishing to produce svg figures)
• biomaRt
• org.Hs.eg.db
• edgeR
• scales
• GSEABase
• limma

Usage

To reproduce the analysis, simply switch to the HCI011_RNAseq/R directory, open an R session and type source("PDX_FOXM1_RNAseq_pub.R")

Figures and tables will be generated under the HCI011_RNAseq/output directory.