Installation of package anRichemnt



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

Prerequisites

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:


source("https://bioconductor.org/biocLite.R");
biocLite(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

Installation of the package 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/anRichmentMethods and path/to/anRichment with the directory and filename of the downloaded package):


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


The packages should be automatically unpacked and installed.

Troubleshooting



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