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.
The WGCNA package requires the following packages to be installed: stats, grDevices, utils, matrixStats (0.8.1 or higher), Hmisc, splines, foreach, doParallel, fastcluster, dynamicTreeCut, survival, parallel, preprocessCore, GO.db, impute, and AnnotationDbi. If your system does not have them installed, the easiest way to install them is to issue the following command at the R prompt:
If you have an old version of R for which BiocManager is not available, you can replace the BiocManager::install call by
If you plan on using annotation capabilities (such as
GOenrichmentAnalysis), we also
installing Bioconductor annotation packages. This can be accomplished by the following R commands:
Replace the call to BiocManager::install by biocLite if the former is not available. If you run an older version of R, the above may not install the newest version of the dynamicTreeCut package. Should you encounter this problem, please manually download and install dynamicTreeCut from this web page.
Installation of the package is simple. Download the appropriate package file from the
download page and save it in a directory of your choice. 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/file with the
directory and filename of the downloaded package):
For Mac users: if you are compiling and installing a source package, add the argument
install.packagescommand. The additional argument should not be supplied if you are installing the pre-compiled binary bundle (.tgz file). The packages should be automatically unpacked and installed. If you have trouble installing the package, make sure you have installed Apple Xcode Tools, including Xcode command line tools, available from http://developer.apple.com, installed. See the R documentation on http://cran.r-project.org, in particular this section for more details on installation of source packages on OS X.
If you do not have sufficient privileges, you can either (1) ask your system administrator to install the
packages for you, or (2) create your own personal R library. You may also wish to create a separate
R library to hold oder versions of these and/or other packages. To do that, create a directory on your
system where you want the library to reside. Then run an R session, and at the prompt type (replace
path/to/file with the
directory and filename of the downloaded package and
path/to/library with your library directory)
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