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install_libraries.R
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install_libraries.R
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#! /usr/bin/env Rscript
######################################################################################################
####################### LIBRARY INSTALLING SCRIPT for DEgenes Hunter #################################
######################################################################################################
###############
###############
#For using type source("install_libraries.R") in your R console (version R-3.2.3 or higher)
############## Installing latest version of Bioconductor #####################
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite()
#################### LIBRARIES FOR DIFFERENTIAL EXPRESSION ANALYSIS SCRIPT (degenes_Hunter.R) ############
print("Installing libraries for differential expression analysis script")
## PACKAGES IN CRAN
install.packages(c("ggplot2","VennDiagram","gplots","optparse","stringr","plyr"))
## PACKAGES IN BIOCONDUCTOR
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("limma")
biocLite("edgeR")
biocLite("DESeq2")
biocLite("NOISeq")
#################### LIBRARIES required specifically by the FUNCTIONAL ANALYSIS SCRIPT (functional_Hunter.R) ############
print("Installing additional libraries for functional analysis script")
## PACKAGES IN BIOCONDUCTOR
## try http:// if https:// URLs are not supported
## Functional analysis script requires "optparse", "stringr" and "plyr" as well.
source("https://bioconductor.org/biocLite.R")
biocLite("biomaRt")
biocLite("topGO")
biocLite("KEGGREST")