3.4.4. Installing a package from Bioconductor#

You can search the Bioconductor software package list on the website (currently has 1974 packages). Once you have identified a package to install, you can follow the steps below to install it.

I will install the edgeR package as an example.

Install package using BiocManager::install() command#

  1. Start an R session.

  2. Install the BiocManager package. This is necessary for installing R packages from Bioconductor repository.

    Note

    You only need to do this once.

    The next time you wish to install a package from Bioconductor, you can proceed to step 3.

  3. At the R prompt, use the BiocManager::install() command with the name of the package you would like to install in quotes.

    For example:

    BiocManager::install("edgeR")

    Press the ENTER key to proceed.

    The package and its dependencies will now be downloaded, compiled and installed.

    Output:

    Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'BiocVersion', 'edgeR'
also installing the dependencies ‘limma’, ‘locfit’, ‘Rcpp’
...
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (edgeR)

If there are no errors during the process, the package installation is successful.