Using Bioconductor

The current release of Bioconductor is version 2.14; it works with R version 3.1.0. Users of older R and Bioconductor versions must update their installation to take advantage of new features.

Install the latest release of R, then get the latest version of Bioconductor by starting R and entering the commands

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

Details, including instructions to install additional packages and update packages, are provided below. A devel version of Bioconductor is available.

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.

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Install Bioconductor Packages

Use the biocLite.R script to install Bioconductor packages. To install core packages, type the following in an R command window:

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

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

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

The biocLite() function (in the BiocInstaller package installed by the biocLite.R script) has arguments that change its default behavior; type ?biocLite for further help.

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Find Bioconductor Packages

Visit the Workflows page 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 within your version of Bioconductor, start a new session of R and enter

source("http://bioconductor.org/biocLite.R")
biocLite()                  ## R version 3.0 or later

Use the argument ask=FALSE to update old packages without being prompted. For older versions of R, use the command biocLite(NULL). Read the help page for ?biocLite for additional details.

Upgrading installed Bioconductor packages

Some versions of R support more than one version of Bioconductor. To use the latest version of Bioconductor for your version of R, enter

source("http://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")     ## R version 2.15 or later

Read the help page for ?BiocUpgrade for additional details. Remember that more recent versions of Bioconductor may be available if your version of R is out-of-date.

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, type="source")

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 work flow. It also requires that you have the necessary compilers installed.

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Troubleshoot Package Installations

Use the commands

library(BiocInstaller)
biocValid()             ## R version 3.0 or later

to flag packages that are either out-of-date or too new for your version of Bioconductor. The output suggests ways to solve identified problems, and the help page ?biocValid lists arguments influencing the behavior of the function.

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Bioconductor Release »

Packages in the stable, semi-annual release:


Bioconductor is also available as an Amazon Machine Image.
Fred Hutchinson Cancer Research Center