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
Install the BiocManager package. This is necessary for installing R packages from Bioconductor repository.
You only need to do this once.
The next time you wish to install a package from Bioconductor, you can proceed to step 3.
At the R prompt, use the
BiocManager::install()command with the name of the package you would like to install in quotes.
Press the ENTER key to proceed.
The package and its dependencies will now be downloaded, compiled and installed.
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.