Install Bioconductor

Installing Bioconductor.

Motivation #

The Bioconductor project provides many R packages focused on the analysis of biological assays.

Install BiocManager #

Instructions are available on the main Bioconductor website.

Briefly, first launch RStudio.

Then, run the following command in the R console:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

RTools #

When running the command above, you may be prompted with the following warning message:

In which case, please navigate to https://cran.rstudio.com/bin/windows/Rtools/.

Click on the link ‘RTools x.x’ (where x.x is a version of RTools). In particular, select a version of RTools that matches the version of R that you are currently using.

On the next page, click on the link to download the RTools installer (e.g., this is ‘Rtools42 installer’ for RTools 4.2).

Then, double-click on the installer file that you just downloaded and progress through the screens of the installation program.

We recommend leaving all options to their default values.

We also recommend closing RStudio and launching a new RStudio application.

Install the latest version of Bioconductor #

In the R console of the RStudio application, run the following command:

BiocManager::install()

You should see messages similar to the following.

In this example, Bioconductor version 3.15 was installed, as the latest version of Bioconductor compatible with R 4.2.2.