• Getting The Latest Version of Bioconductor
• Install Packages
• Find Packages
• Update Packages
• Install R

Getting The Latest Version of Bioconductor

If you have installed the latest release of R, you will automatically get packages from the latest version of Bioconductor by following the steps below. The current release version of R is 2.14, and the currently released Bioconductor version is 2.9.

Install Bioconductor Packages

Use the biocLite.R script to install Bioconductor packages. To install a particular package, e.g., limma, type the following in an R command window:

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

Install several packages, e.g., "GenomicFeatures" and "AnnotationDbi", with

biocLite(c("GenomicFeatures", "AnnotationDbi"))

To install a selection of core Bioconductor packages, use

biocLite()

Packages and their dependencies installed by this usage are: Biobase, IRanges, and AnnotationDbi.

The biocLite() function (in the BiocInstaller package installed by thebiocLite.R script) has arguments that change its default behavior:

pkgs
    Character vector of Bioconductor packages to install.
destdir
    File system directory for downloaded packages.
lib
    R library where packages are installed.

You can type ?biocLite for further installation help.

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Find Bioconductor Packages

Visit the Workflows page, /packagesBiocViews taxonomy, and software package list to discover available packages.

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Update Installed Bioconductor Packages

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

source("http://bioconductor.org/biocLite.R")
old.packages(repos=biocinstallRepos())

To update all installed packages that are out of date, start a new session of R and enter

source("http://bioconductor.org/biocLite.R")
biocLite(character(), ask=FALSE)

Read the help page for ?biocLite for additional details.

Recompiling installed Bioconductor packages

Rarely, underlying changes in the operating system require ALL installed packages to be recompiled for source (C or Fortran) compatibility. One way to address this might be to start a new R session and enter

source("http://bioconductor.org/biocLite.R")
pkgs <- rownames(installed.packages())
biocLite(pkgs)

As this will reinstall all currently installed packages, it likely involves a significant amount of network bandwidth and compilation time. All packages are implicitly updated, and the cumulative effect might introduce wrinkles that disrupt your workflow.

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Install R

1. Download the most recent version of R. The R FAQs 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.