# R base installation

cd /v/linux26_x86_64/appl/stat/R/

wget http://ftp.sunet.se/pub/lang/CRAN/src/base/R-2/R-2.9.0.tar.gz

gzip -d R-2.9.0.tar.gz 

tar xvf R-2.9.0.tar

cd R-2.9.0

./configure

make

make check





# R contributed packages installation

wget http://addictedtor.free.fr/packages/fpc_1.1-5.tar.gz

wget http://addictedtor.free.fr/packages/A2R/A2R_0.0-4.tar.gz

wget http://cran.r-project.org/src/contrib/Archive/rda/rda_1.0.1.tar.gz

wget http://www.math.utu.fi/en/research/groups/bio/projects/ROTS_1.1.1.tar.gz

./bin/R

install.packages(pkgs="fpc_1.1-5.tar.gz", repos=NULL)

install.packages(pkgs="A2R_0.0-4.tar.gz", repos=NULL)

install.packages(pkgs="rda_1.0.1.tar.gz", repos=NULL)

install.packages(pkgs="ROTS_1.1.1.tar.gz", repos=NULL)

install.packages(c("Matrix", "lme4", "amap", "ape", "flexclust", "kohonen", "e1071", "sma", "fastICA"), repos="http://cran.r-project.org", dependencies = T)

install.packages(c("aplpack", "corrgram", "deal", "outliers", "pvclust", "zoo", "qvalue", "scrime"), repos="http://cran.r-project.org", dependencies=T)

install.packages(c("XML"), repos="http://cran.r-project.org", dependencies=T)




# Bioconductor software packages installation

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

biocLite()

biocLite(c("ctc", "ssize", "LPE", "Ruuid", "graph", "affyQCReport", "GlobalAncova", "impute", "idiogram", "GOstats", "beadarray", "simpleaffy", "globaltest"))

biocLite(c("geneplotter", "biomaRt", "lumi", "prada", "siggenes", "plier")) 

biocLite(c("cosmo", "beadarraySNP", "GEOquery", "ArrayExpress"))

biocLite(c("GeneCycle", "GeneNet", "GenomeGraphs"))

biocLite(c("MLInterfaces"))

biocLite(c("PAnnBuilder", "oligoClasses"))

biocLite(c("matchprobes"))

biocLite(c("statmod", "vegan", "safe", "oligo"))

 

# Annotation packages for Affymetrix

source("http://www.bioconductor.org/biocLite.R")
setRepositories(ind=c(4))
b<-available.packages()
d<-b[-grep("BSgenome", rownames(b)),]
install.packages(d)


# Install BrainArray packages for Affymetrix Gene ST (is this needed? yes, unless the whole BrainArray is downloaded)

quit(save="no")

wget http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/entrezg.download/hugene10stv1hsentrezgcdf_11.0.1.tar.gz
wget http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/entrezg.download/hugene10stv1hsentrezgprobe_11.0.1.tar.gz
wget http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/entrezg.download/hugene10stv1hsentrezg.db_11.0.1.tar.gz

./bin/R CMD INSTALL hugene10stv1hsentrezgcdf_11.0.1.tar.gz
./bin/R CMD INSTALL hugene10stv1hsentrezgprobe_11.0.1.tar.gz
./bin/R CMD INSTALL hugene10stv1hsentrezg.db_11.0.1.tar.gz

wget http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/entrezg.download/mogene10stv1mmentrezgcdf_11.0.1.tar.gz
wget http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/entrezg.download/mogene10stv1mmentrezgprobe_11.0.1.tar.gz
wget http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/entrezg.download/mogene10stv1mmentrezg.db_11.0.1.tar.gz

./bin/R CMD INSTALL mogene10stv1mmentrezgcdf_11.0.1.tar.gz
./bin/R CMD INSTALL mogene10stv1mmentrezgprobe_11.0.1.tar.gz
./bin/R CMD INSTALL mogene10stv1mmentrezg.db_11.0.1.tar.gz

wget http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/entrezg.download/ragene10stv1rnentrezgcdf_11.0.1.tar.gz
wget http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/entrezg.download/ragene10stv1rnentrezgprobe_11.0.1.tar.gz
wget http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/entrezg.download/ragene10stv1rnentrezg.db_11.0.1.tar.gz

./bin/R CMD INSTALL ragene10stv1rnentrezgcdf_11.0.1.tar.gz
./bin/R CMD INSTALL ragene10stv1rnentrezgprobe_11.0.1.tar.gz
./bin/R CMD INSTALL ragene10stv1rnentrezg.db_11.0.1.tar.gz

# Done! You should remove downloaded tar.gz-files...