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packages.R
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packages.R
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# commands to install needed R packages
# sudo R -f packages.R
install.packages('getopt', repos='http://cran.us.r-project.org')
install.packages('ggplot2', repos='http://cran.us.r-project.org')
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
if(!require('glmnet')) {
install.packages('glmnet')
library(glmnet)
}
if(!require('sva')) {
biocLite("sva")
library(sva)
}
if(!require('gplots')) {
install.packages('gplots')
library(gplots)
}
if(!require('samr')) {
biocLite("impute")
install.packages('samr')
library(samr)
}
if(!require('plyr')) {
install.packages('plyr')
library(plyr)
}
if(!require('topGO')) {
biocLite("topGO")
library(topGO)
}
if(!require('goseq')) {
biocLite("goseq")
library(goseq)
}
if(!require('dplyr')) {
install.packages('dplyr')
library(dplyr)
}
if(!require('knitr')) {
install.packages('knitr')
library(knitr)
}
if(!require('broom')) {
install.packages('broom')
library(broom)
}
if(!require('biobroom')) {
biocLite("biobroom")
library(biobroom)
}
if(!require('tidyr')) {
install.packages('tidyr')
library(tidyr)
}
if(!require('qvalue')) {
biocLite("qvalue")
library(qvalue)
}
if(!require('edgeR')) {
biocLite("edgeR")
library(edgeR)
}
if(!require('biomaRt')) {
biocLite("biomaRt")
library(biomaRt,pos = "package:base")
}
if(!require('reshape2')) {
install.packages('reshape2')
library(reshape2)
}
if(!require('devtools')) {
install.packages('devtools')
library(devtools)
}
if(!require('org.Hs.eg.db')) {
biocLite("org.Hs.eg.db")
}