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High-Grade Serous Ovarian Cancer Subtypes - Cellular Deconvolution Through ssGSEA

Summary

This repository contains a procedure that can be used to apply ssGSEA analysis to existing gene expression and subtyping data for hgsc datasets. The experimental data set used in this example was produced by The Cancer Genome Atlas (2011) and is available from BioConductor's curatedOvarianData package. The same procedure should be applicable and easily adaptible to other hgsc datasets and those from other diseases.

Reproduction

Step 1: Download signature gene file

You will need Supplementary Table S1 from Newman et al. 2015.

Please download the file. Copy A3:W550 and paste into A1 of a new spreadsheet. Save this file as '/data/raw/LM22_DEG.csv'.

Step 2: Run analysis pipeline

Run ANALYSIS.sh

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