# | eval: false
install.packages("BiocManager")
::install(c("WGCNA", "devtools"))
BiocManagerlibrary(devtools)
install_github('jdrudolph/PerseusR')
WGCNA
1 Weighted Gene Co-expression Network Analysis
This package is provided through the R-language integration into Perseus and therefore requires R as well as the package itself to be installed in order to be used. Visit the PluginInterop and PerseusR for additional technical information on the integration of R and Perseus.
2 Installation
- Download the R installer install it.
- Remember the R installation directory. If you do not know where you have installed R, check the default location
C:\Program Files\R\R-3.5.0\bin
, or search forRscript.exe
. - Add R to your
Path
environment variable. Open the start menu and search for “environment variables”, and select “Edit system environment variables”. - Find the
Path
variable in the editor and selectEdit
. - Now we can add R to the
Path
by clickingNew
and entering the location of the.../bin
folder of the R installation, e.gC:\Program Files\R\R-3.5.0\bin
. - In certain Windows version you might have to edit the
Path
directly. ThePath
consists of folder locations separated by ‘;’. Therefore, just append the installation location of R and the ‘;’ separator. No spaces or quotes are required. If thePath
variable is not defined on your system, you can define it yourself. - Check that R is installed correctly by opening
cmd.exe
from the start menu and enteringR
An R session should start. - Inside the running R session, install the WGCNA and PerseusR libraries by entering/pasting the following code line-by-line. When prompted for local install, type ‘yes’ twice and select a close-by server for the package download.
- You should now be able to load the
WGCNA
andPerseusR
libraries by entering the following code. Upon loading,WGCNA
will print some output, whilePerseusR
will not print any.
# | eval: false
library(WGCNA)
library(PerseusR)
You are now ready to perform co-expression analysis from within Perseus.