Chapter 4 Bioconductor Packages
While most packages for R are obtained from CRAN, R packages designed specifically for Bioinformatics work are typically hosted on the Bioconductor site (Bioconductor.org 2021), which hosts free open source software for bioinformatics.
We will need to use some Bioconductor packages in Computer Lab 8B.
Please run the code in the section below prior to beginning Computer Lab 8B. The Bioconductor packages can take a while to install, so it’s important that these are all installed on your system before you start the lab.
4.1
In order to download and install Bioconductor R packages, we have to use a slightly different procedure to normal.
To begin, we need to install the BiocManager package, which we will use to install specific Bioconductor packages. Run the code below to install this package.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.14")Once this has installed, we can use the command BiocManager::install to install specific Bioconductor packages. Run the code below to install the R packages we will require for our work in Computer Lab 8B.
Note: Some of these packages might be installed as part of the installation process of a preceding package, but it’s best to be safe.
BiocManager::install(c("edgeR", "qvalue", "GenomicAlignments", "GenomicFeatures"))4.2
If the message
Update all/some/none? [a/s/n]:
appears in your console window, type a in the console and hit Enter. This should update all the relevant packages.
Note: It might not be strictly necessary to update all these packages, but generally speaking it is a good idea to always be using the latest (stable) version of an R package.