R - BioConductor and other libraries | Research IT Core Services

After R is installed, this is how to install the BioConductor libraries. Mind you, it takes several hours to get done.

> source("http://www.bioconductor.org/getBioC.R")

> getBioC()

To check for all the installed libraries in a R system,

> library()

For installing specific packages (like impute, mclust etc.),

> install.packages("impute")

Important libraries include:

affycoretools, affycomp (Chunyan Liu)

getBioC(c("affycoretools","affycomp"))

affyQCReport (Walter Jessen, Chunyan Liu)

Download source (*.tgz) from http://bioconductor.org/packages/1.8/bioc/html/affyQCReport.html
R CMD INSTALL <download folder>/<source.tgz>

Category (Chunyan Liu)

getBioC(c("Category"))

caTools (Rachana Jain)

install.packages("caTools")

ccrel (Lisa Martin and Meredith Tabangin)

Download the source from http://www.stat.auckland.ac.nz/~browning/ccrel/ccrel.htm
tar zxf CCREL_PACKAGEv0_3.tar.gz
cd CCREL_PACKAGE
make
cp -R ccrel.lib/ccrel $RHOME/lib/R/library/.
Start R by typing R
check if ccrel is available by checking library()

gcrma (Walter Jessen)

Start R in the system.
> source("http://www.bioconductor.org/getBioC.R")
> getBioC(c("gcrma"))
This process gets the correct version of the packages for the running version of Bioconductor package in the system

glmpath (Xiangdong Liu)

install.packages("glmpath")

GO (Chunyan Liu)

getBioC(c("Category"))

hgfocus[cdf/probe], hgu133a[cdf/probe], hgu133b[cdf/probe], hgu133plus2cdf (Walter Jessen)

Start R in the system.
> source("http://www.bioconductor.org/getBioC.R")
> getBioC(c("hgfocuscdf", "hgfocusprobe", "hgu133acdf, "hgu133aprobe", "hgu133bcdf, "hgu133bprobe", "hgu133plus2cdf"))
This process gets the correct version of the packages for the running version of Bioconductor package in the system

hgu133plus2 (Chunyan Liu)

getBioC(c("hgu133plus2"))

Hmisc (Johannes Freudenberg)

install.packages("Hmisc")

hs133ahsrefseq8[cdf/probe] (Walter Jessen)

download source (*.tgz) from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download_v8.asp
R CMD INSTALL <download folder>/<source.tgz>

hs133av2hsrefseq8[cdf/probe] (Johannes Freudenberg)

Obtained source (*.tar.gz) from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download_v8.asp
R CMD INSTALL <download folder>/<source.tgz>

hs133bhsrefseq8[cdf/probe], hs133phsrefseq[cdf/probe] (Walter Jessen)

download source (*.tgz) from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download_v8.asp
R CMD INSTALL <download folder>/<source.tgz>

hs133phsrefseq8[cdf/probe] (Johannes Freudenberg)

Obtained source (*.tar.gz) from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download_v8.asp
R CMD INSTALL <download folder>/<source.tgz>

hsex10stv2hsrefseq8[cdf/probe] (Johannes Freudenberg)

Obtained source (*.tar.gz) from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdf8/hsex10stv2hsrefseq8cdf_8.0.0.tar.gz
R CMD INSTALL <download folder>/<source.tgz>

humanLLMappings (Maureen Sartor & Mario Medvedovic)

getBioC(c("humanLLMappings"))

impute (Baoqiang Cao)

install.packages("impute")

KEGG (Chunyan Liu)

getBioC(c("KEGG"))

mm430ammrefseq[cdf/probe], mm430a2mmrefseq[cdf/probe], mm430mmrefseq[cdf/probe], moe430a[cdf/probe], mouse4302cdf (Walter Jessen)

source("http://www.bioconductor.org/getBioC.R")
getBioC(c(""))

pamr (Chunyan Liu)

getBioC(c("pamr"))

qtl (Daniel Prows)

install.packages("qtl")

randomForest (Johannes Freudenberg)

install.packages("randomForest")

RColorBrewer (Chunyan Liu)

getBioC(c("RColorBrewer"))

Rcmdr (Lukasz Itert)

install.packages("Rcmdr")

RMySQL (Kaustubh Shinde)

install.packages("RMySQL")

RSPerl (Rachana Jain & Mukta Phatak)

Download source (*.tgz) from http://www.omegahat.org/RSPerl/ to /tmp
cd /tmp && tar zxf RSPerl_*.tgz
R CMD INSTALL --configure-args='--with-in-perl' RSPerl
This installs the library under /usr/local/encap/R-***/lib/R/library
The Perl library goes inside /usr/local/encap/R-***/lib/R/library/RSPerl/perl.
Use the scripts inside /usr/local/encap/R-***/lib/R/library/RSPerl/scripts to define necessary variables before using this module.

sigPathway (Maureen Sartor & Mario Medvedovic)

Download source (*.tar.gz) from http://bioconductor.org/packages/1.9/bioc/html/sigPathway.html
R CMD INSTALL <download folder>/<source.tgz>

simpleaffy (Walter Jessen, Chunyan Liu)

Download source (*.tgz) from http://bioinformatics.picr.man.ac.uk/simpleaffy/
R CMD INSTALL <download folder>/<source.tgz>

tkWidgets (Walter Jessen, Chunyan Liu)

Download source (*.tgz) from http://www.bioconductor.org/repository/release1.5/package/html/tkWidgets.html
R CMD INSTALL <download folder>/<source.tgz>

tree (Rachana Jain)

install.packages("tree")

Issue faced here

When R was initially installed in protein (through frontier), frontier did not have tk-dev packages. Hence Tcl/Tk support was not built in R.

You can check this by typing capabilities() inside R and see what it says under TCLTK.

So I am rebuilding R under protein's encap after installing tk-devel in frontier.

widgetTools (Chunyan Liu)

getBioC(c("widgetTools"))

Mm430A

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdf9/mm430ammrefseqcdf_9.0.1.tar.gz http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdf9/mm430ammrefseqprobe_9.0.1.tar.gz

Mouse Genome 430A 2.0 http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdf9/mm430a2mmrefseqcdf_9.0.1.tar.gz http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdf9/mm430a2mmrefseqprobe_9.0.1.tar.gz

Hs133P http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdf9/hs133phsrefseqcdf_9.0.1.tar.gz http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdf9/hs133phsrefseqprobe_9.0.1.tar.gz