Ensemble of Gene Set Enrichment Analyses

_{Credit: Roberto Bonelli}

This package is part of the Bioconductor project and implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing.

Author: Monther Alhamdoosh, Luyi Tian, Milica Ng and Matthew Ritchie

Maintainer: Monther Alhamdoosh <m.hamdoosh at gmail.com>

Citation (from within R, enter citation("EGSEA")):

Alhamdoosh M, Ng M, Wilson N, Sheridan J, Huynh H, Wilson M and Ritchie M (2017). “Combining multiple tools outperforms individual methods in gene set enrichment analyses.” Bioinformatics, 33(3). doi: 10.1093/bioinformatics/btw623.

Alhamdoosh M, Law CW, Tian L et al. Easy and efficient ensemble gene set testing with EGSEA [version 1; peer review: 1 approved, 3 approved with reservations]. F1000Research 2017, 6:2010. doi: 10.12688/f1000research.12544.1

Installation

To install the stable release of this package, start R and enter:

## try http:// if https:// URLs are not supported
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("EGSEA")

To install the development version of this package, start R and enter:

install.packages("devtools") # if you have not installed "devtools" package
devtools::install_github("malhamdoosh/EGSEA")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("EGSEA")