b05-installing_bioconductor_AC01.RmdR packages (aka “libraries”) can live in many places. Most are accessed via CRAN, the Comprehensive R Archieve Network. The bioinformatics and computational biology community also has its own package hosting system called Bioconductor.
NOTE: If you are working in an RStudio Cloud environment organized by someone else (eg a course instructor), they likely are taking care of most of package management issues, inlcuding setting up Bioconductor. The following information is still useful to be familiar with.
To interface with Bioconductor you need the BiocManager package. The Bioconductor people have put BiocManager on CRAN to allow you to set up interactions with Bioconductor.
Note that if you have an old version of R you will need to upate it to interact with bioconductor.
BiocManager can be installed using the install.packages() packages command.
Once downloaded, BioManager needs to be explicitly loaded into your active R session
Individual packages can then be downloaded using the install() command.
Bioconductor has many dependencies - other packages which is relies on. When you install Bioconductor packages you may need to update these packages. If something seems to not be working during this process, restart R and being the Bioconductor installation process until things seem to work.
Again, to actually load the Biostrings package into your active R sessions requires the libary() command:
For more information on BiocManager see the vignette: https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html