drmjc/metaGSEA: Meta-analysis of GSEA analyses, including intra- and inter-experiment comparisons

A collection of R and bash code to simplify the down-stream analysis of GSEA results. Efficient methods for importing and storing GSEA outputs, comparing genesets within a single GSEA run, and comparing genesets between different GSEA runs. Useful visualisation is the key strength of this package, utilising GSEA bar plots, correspondence at the top (CAT) plots, and hierarchical clustering plots of geneset similarities. Also the ability to clean up GSEA output on unix-alike systems, by improving the GSEA pre-ranked output, and the gene tables in each GSEA report by including the gene symbol, description and hyperlinks to Entrez Gene. This has evolved into a suite of code for importing/exporting/subsetting many of the GenePattern file types (GCT, CLS, CLM, CHIP, RES, ODF)

Getting started

Package details

AuthorMark Cowley
MaintainerMark Cowley <[email protected]>
LicenseGPL-2
Version1.1.3
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("drmjc/metaGSEA")
drmjc/metaGSEA documentation built on May 15, 2019, 2:24 p.m.