README.md

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

metaGSEA

An R package for I/O of GenePattern datatypes, and running meta-GSEA analyses

Description

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)

See also

This code empowers the metaGSEA GenePattern module, available at http://pwbc.garvan.unsw.edu.au/gp

Future Plans

• split the package into genepatternIO and metaGSEA
• add S3 or S4 datatypes for at least GCT, CHIP, CLS objects.

Installation

install.packages(c("XML", "gplots", "stringr", "devtools"))
source("http://bioconductor.org/biocLite.R")
biocLite(c("Biobase", "GSEABase"))
library(devtools)
install_github("excelIO", "drmjc")
install_github("mjcbase", "drmjc")
install_github("mjcgraphics", "drmjc")
install_github("microarrays", "drmjc")
install_github("mjcstats", "drmjc")
install_github("mjcstats", "genomics")

Usage

Extensive package documentations is available via:

library(metaGSEA)
?metaGSEA

drmjc/metaGSEA documentation built on Aug. 8, 2020, 1:53 p.m.