jshilts / metapredict

metapredict R package

metapredict

metapredict enables meta-analysis of gene expression using the elastic net (i.e., glmnet). For technical details, please check out the paper.

Installation

Install the package in your local version of R:

source('https://bioconductor.org/biocLite.R')
biocLite(c('org.Hs.eg.db', 'org.Mm.eg.db', 'org.Dr.eg.db'))
install.packages('devtools')
devtools::install_github('jakejh/metapredict', repos=BiocInstaller::biocinstallRepos())

Or use a pre-built docker image, which has all dependencies already installed:

docker pull jakejh/hugheyverse

Getting started

First follow the instructions to download and prepare the data for the example meta-analysis.

file.show(system.file('extdata', 'prepare_example.html', package='metapredict'))

Then work through the example meta-analysis.

file.show(system.file('extdata', 'run_example.html', package='metapredict'))

Finally, consult the detailed guide to running your own meta-analysis.

file.show(system.file('extdata', 'guide.html', package='metapredict'))