Install R

1. Download the most recent version of R from The Comprehensive R Archive Network (CRAN). The R FAQ and the R Installation and Administration Manual contain detailed instructions for installing R on various platforms (Linux, OS X, and Windows being the main ones).
2. Start the R program; on Windows and OS X, this will usually mean double-clicking on the R application, on UNIX-like systems, type "R" at a shell prompt.
3. As a first step with R, start the R help browser by typing "help.start()" in the R command window. For help on any function, e.g. the "mean" function, type "? mean".

Install standard Bioconductor packages

Install BioConductor packages using the biocLite.R installation script. In an R command window, type the following:

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

This installs the following packages: affy, affydata, affyPLM, annaffy, annotate, Biobase, Biostrings, DynDoc, gcrma, genefilter, geneplotter, hgu95av2.db, limma, marray, matchprobes, multtest, ROC, vsn, xtable, affyQCReport. After downloading and installing these packages, the script prints "Installation complete" and TRUE.

The biocLite script has arguments that change the default behavior:

pkgs

Character vector of BioConductor packages to install.

destdir

File system directory for downloaded packages.

lib

R library where packages are installed.

Install additional Bioconductor packages

There are many Bioconductor and R packages in addition to those in the default installation of biocLite. A catalog of the Bioconductor packages is available at BiocViews. To install a new package, e.g., EBImage, use

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

Install "pkg1" and "pkg2" with

biocLite(c("pkg1", "pkg2"))

Install package groups

In special circumstances, a particular predefined group of packages can be installed. The following groups are available:

default

This defines the packages that are installed when biocLite is invoked with no additional arguments.

lite

Essential packages for very low-bandwidth connections.

affy

A selection of packages particularly useful in analysis of Affymetrix expression arrays.

graph

Packages useful for graph-based algorithms and representations.

monograph

Packages for use with the book Bioinformatics and Computational Biology Solutions Using R and Bioconductor.

RBioinf

Packages for use with the book Bioinformatics with R.

all

All software packages; this is a very large installation and not recommended for most users.

To install a group of packages, use a command such as

biocLite(groupName="RBioinf")

Update installed Bioconductor packages

Bioconductor packages, especially those in the development branch, are updated fairly regularly. To update all of your installed packages, start a new session of R and enter

source("http://bioconductor.org/biocLite.R")
update.packages(repos=biocinstallRepos(), ask=FALSE)

Read the help page for update.packages for additional details.

Additional resources

• BioC Release Packages
• BioC Development Packages (requires R-devel)
• Metadata
• Experiment data
• Mirrors