Technical prerequisites for Bioinformatics research in R, RStudio and Ubuntu 14.04 LTS or Windows (64-bit versions)

Posted: 2014/10/18 in Data Science, Ubuntu
Tags: , , , ,

Purpose of these lists is to clarify which applications and R packages need to be installed on your PC to be able to perform bioinformatics research in Ubuntu 14.04 LTS or Windows (64-bit versions)

Order of installation of applications in Windows, Mac OS X or GNU/Linux before installing packages in R 3.1.1 or newer:

* libxml2-devel in Fedora 20 (=GNU/Linux distribution)
* gcc gcc47-c++ gcc-fortran in OpenSuse (=GNU/Linux distribution)
* gcc g++ gfortran xmlsec1 libxml2-dev libcurl4-openssl-dev r-cran-rcurl curl in Ubuntu 14.04 LTS 32-bit or 64-bit (=GNU/Linux distribution)
* R 3.1.1 or newer
* Windows 64-bit users should run the following .cmd script as administrator:

The previous .cmd script takes care of installing curl,R,RStudio and other applications in Windows. Or you can download curl here:

* Google Chrome browser or any other browser that uses the newest version of Adobe Flash in Windows, Mac OS X and GNU/Linux:
* RStudio is optional, but recommended:
* I recommend avoiding RKWard (as R extension), as it seems to have issues with R 3.1.1 in combination with BioConductor packages.

Order of installation of R packages in R 3.1.1 (or newer) after installing previous applications in Ubuntu 14.04 LTS or Windows (64-bit versions):

* XML (requires install first of libxml2-dev or libxml2-devel in GNU/Linux)
* RJSONIO (requires install first of gcc and gcc47-c++ in OpenSuse and install of g++ in Ubuntu)
* Rcpp (requires R version >= 3.0.0 !)
* httr (requires R version >= 3.0.0 !)
* maps
* reshape2
* RCurl (requires install first of curl binary on operating system level)
* devtools (is required to install sweSCB R package from Github)
* sweSCB (install from github, requires install first of devtools R package)
* calibrate
* pheatmap
* gplots
* Biobase,BioConductor package, installed through biocLite()
* DESeq2 ,BioConductor package, installed through biocLite()
* biomaRt ,BioConductor package, installed through biocLite()
* ,BioConductor package, installed through biocLite()
* topGO ,BioConductor package, installed through biocLite()
* for those who want to do the extended, non-mandatory version of the lab: Rsubread is a BioConductor package which is not available on Windows. If you are on Windows, just do the short version of the lab. Rsubread only works on Linux and Mac OS X 32-bit and 64-bit systems.
* Rgraphviz,BioConductor package, installed through biocLite()
* GEOquery,BioConductor package, installed through biocLite()
* limma,BioConductor package, installed through biocLite()

Copy-paste each line below one line at a time into R or RStudio. Hit the ENTER key between each line.

install.packages("Rcpp", dependencies = TRUE)
install.packages("devtools", dependencies = TRUE)

# install bioconductor packages
# warning: compiling DESeq2 may take a long time
# do NOT interrupt the process!


# run following biocLite("BiocUpgrade") 
# if you are upgrading from an older Bioconductor version
# to Bioconductor version 3.0 (BiocInstaller 1.16.0)
# The current release of Bioconductor is version 3.0 
# it works with R version 3.1.1
# Users of older R and Bioconductor versions must update their installation
# to take advantage of new features.


Here is more info about installing the curl binary:



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