Installation of add-on packages downloaded from our websites



This is a short description of the installation of the packages you can download from the main site and sites referenced from there. For more details, please take a look at the manuals provided by the R project.

Packages anRichmentMethods and anRichment can be installed using an easy to use installation script. Open an R session and type (or copy and paste) the following commands:

source("https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/GeneAnnotation/installAnRichment.R");
installAnRichment();

If this installation script fails, please examine the error message and try correcting the indicated problem. If that fails, please try the manual installation below or contact Peter Langfelder, including the error message and output of the command sessionInfo().

Manual installation

Prerequisites

Add-on packages for anRichment require, unsurprisingly, the anRichment package to be installed.

The anRichment package requires the following packages to be installed: WGCNA, AnnotationDbi, GO.db, XML, the transcript DB packages TxDb.Hsapiens.UCSC.hg19.knownGene and TxDb.Mmusculus.UCSC.mm10.knownGene, and any applicable org.Xx.eg.db packages (org.Hs.eg.db and org.Mm.eg.db are mandatory dependencies). If your system does not have them installed, the easiest way to install them is to issue the following command at the R prompt:


install.packages("BiocManager")
BiocManager::install(c("AnnotationDBI", "GO.db", "org.Hs.eg.db", "org.Mm.eg.db",
"XML", "WGCNA", "TxDb.Hsapiens.UCSC.hg19.knownGene",
"TxDb.Mmusculus.UCSC.mm10.knownGene"));

Please be patient; if these packages are installed for the first time, a large number of dependecies need to be downloded and installed, but the process eventually finishes.

Installation of packages anRichmentMethods and anRichment and their extensions

Installation of the packages is simple. Download the appropriate package file from the download page and save it in a directory of your choice. Make sure your download manager does not automatically uncompress the file. Run an R session as a user with sufficient privileges to install software (see below if you don't have the requisite privileges). At the prompt, type (replace path/to/package with the directory and filename of the downloaded package):


install.packages("path/to/package", repos = NULL, type = "source");


The package should be automatically unpacked and installed.

Troubleshooting



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