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:
- 1.1 affycoretools, affycomp (Chunyan Liu)
- 1.2 affyQCReport (Walter Jessen, Chunyan Liu)
- 1.3 Category (Chunyan Liu)
- 1.4 caTools (Rachana Jain)
- 1.5 ccrel (Lisa Martin and Meredith Tabangin)
- 1.6 gcrma (Walter Jessen)
- 1.7 glmpath (Xiangdong Liu)
- 1.8 GO (Chunyan Liu)
- 1.9 hgfocus[cdf/probe], hgu133a[cdf/probe], hgu133b[cdf/probe], hgu133plus2cdf (Walter Jessen)
- 1.10 hgu133plus2 (Chunyan Liu)
- 1.11 Hmisc (Johannes Freudenberg)
- 1.12 hs133ahsrefseq8[cdf/probe] (Walter Jessen)
- 1.13 hs133av2hsrefseq8[cdf/probe] (Johannes Freudenberg)
- 1.14 hs133bhsrefseq8[cdf/probe], hs133phsrefseq[cdf/probe] (Walter Jessen)
- 1.15 hs133phsrefseq8[cdf/probe] (Johannes Freudenberg)
- 1.16 hsex10stv2hsrefseq8[cdf/probe] (Johannes Freudenberg)
- 1.17 humanLLMappings (Maureen Sartor & Mario Medvedovic)
- 1.18 impute (Baoqiang Cao)
- 1.19 KEGG (Chunyan Liu)
- 1.20 mm430ammrefseq[cdf/probe], mm430a2mmrefseq[cdf/probe], mm430mmrefseq[cdf/probe], moe430a[cdf/probe], mouse4302cdf (Walter Jessen)
- 1.21 pamr (Chunyan Liu)
- 1.22 qtl (Daniel Prows)
- 1.23 randomForest (Johannes Freudenberg)
- 1.24 RColorBrewer (Chunyan Liu)
- 1.25 Rcmdr (Lukasz Itert)
- 1.26 RMySQL (Kaustubh Shinde)
- 1.27 RSPerl (Rachana Jain & Mukta Phatak)
- 1.28 sigPathway (Maureen Sartor & Mario Medvedovic)
- 1.29 simpleaffy (Walter Jessen, Chunyan Liu)
- 1.30 tkWidgets (Walter Jessen, Chunyan Liu)
- 1.31 tree (Rachana Jain)
- 1.32 widgetTools (Chunyan Liu)
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