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R - BioConductor and other libraries

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

> source("")

> 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)

Category (Chunyan Liu)

  • getBioC(c("Category"))

caTools (Rachana Jain)

  • install.packages("caTools")

ccrel (Lisa Martin and Meredith Tabangin)

gcrma (Walter Jessen)

  • Start R in the system.
  • > source("")
  • > 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("")
  • > 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)

hs133av2hsrefseq8[cdf/probe] (Johannes Freudenberg)

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

hs133phsrefseq8[cdf/probe] (Johannes Freudenberg)

hsex10stv2hsrefseq8[cdf/probe] (Johannes Freudenberg)

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)

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 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)

simpleaffy (Walter Jessen, Chunyan Liu)

tkWidgets (Walter Jessen, Chunyan Liu)

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"))


Mouse Genome 430A 2.0