Install Bioconductor for the first time

Welcome

Welcome to the Bioconductor community!

This guide details how to install the latest release of Bioconductor on your computer for the first time.

This process is different from updating your Bioconductor installation, which will be described in a separate guide (coming soon).

Install R

The current release of Bioconductor is version 3.16; it works with version 4.2. Users of older versions must update their installation to take advantage of new features and to access packages that have been added to Bioconductor since the last release.

Windows

  • Navigate to the CRAN website.
  • Follow the links ‘Download R for Windows’ and ‘install R for the first time’.
  • Click the link ‘Download R-x.x.x for Windows’ (x.x.x being the latest version of ).
  • Run the .exe file that was just downloaded.

macOS

  • Navigate to the CRAN website.
  • Follow the link ‘Download R for macOS’.
  • Click on the .pkg file to download the latest version.
  • Double click on the downloaded file to install .

Additionally:

  • It is also a good idea to install XQuartz (needed by some packages).

Linux

  • Navigate to the CRAN website.
  • Next to the link ‘Download R for Linux’, click on the name of your Linux distribution.
  • Follow the instructions on the web page.

The CRAN web pages provide information to get the most recent version of for common distributions. For most distributions, you could use your package manager (e.g., for Debian/Ubuntu run sudo apt-get install r-base, and for Fedora sudo yum install R), but we don’t recommend this approach as the versions provided by this are usually out of date.

Install the BiocManager package

The BiocManager package is a convenient tool distributed on the CRAN repository to install and update Bioconductor packages.

To install the package, type the following in an console:

> install.packages("BiocManager")

Install the current Bioconductor release

To install the latest version of Bioconductor core packages, type the following in an console:

> BiocManager::install(version = "3.16")

Check your installation

To check your installation, restart your session, and type the following in the console:

> BiocManager::version()
[1] '3.16'

Final words

Congratulations! You are ready to install the latest version of more Bioconductor packages!

Last updated: 2022-11-29 (Last compiled: 2022-12-23)