Difference between revisions of "R installation"
From BioUML platform
Tagir Valeev (Talk | contribs) m ({{R}} used; Category:R added) |
Ivan Yevshin (Talk | contribs) |
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* Rserve: | * Rserve: | ||
apt-get install r-cran-rserve | apt-get install r-cran-rserve | ||
| + | * Set high enough socket connection timeout, add following line to /etc/R/Rprofile.site | ||
| + | options(timeout=864000L); | ||
* BioConductor (from R-console): | * BioConductor (from R-console): | ||
source("http://bioconductor.org/biocLite.R") | source("http://bioconductor.org/biocLite.R") | ||
Revision as of 13:03, 22 April 2013
This page describes how to install R for BioUML. You need to perform the following steps:
- R itself:
yum install R
or
apt-get install r-recommended
- Rserve:
apt-get install r-cran-rserve
- Set high enough socket connection timeout, add following line to /etc/R/Rprofile.site
options(timeout=864000L);
- BioConductor (from R-console):
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("makecdfenv", lib="/usr/local/lib/R/site-library")
- Illumina normalization (from R-console):
biocLite("lumi")
Note that this step may require installation of additional packages in the system like libxml2-dev, libglut3-dev, libcurl4-gnutls-dev.
- Agilent normalization (from R-console):
biocLite("limma")
