1 What is Bioconductor?

  • Covers a wide range of domains:
    • sequencing (RNA-seq, ChIP-seq, single-cell analysis, variant calling, …)
    • microarrays (methylation, gene expression, copy number, …)
    • flow and mass cytometry
    • proteomics
    • imaging
  • There is a core team which, among other things, oversees the project, reviews new package submissions, develops and maintains core infrastructure and maintains daily building and checking of all packages
  • Most packages are contributed by the community

2 How to install Bioconductor packages

  • Detailed instructions are available online
  • There is a new Bioconductor release twice per year (typically April and October)
  • Between those times, development is going on in the parallel devel branch
  • Do not mix packages from different releases!
  • The available Bioconductor releases also depend on your version of R - if you want the latest Bioconductor packages, you need the latest version of R.
  • Bioconductor packages (and also packages hosted on CRAN or GitHub) are installed using the BiocManager CRAN package:
install.packages("BiocManager")
BiocManager::install("limma")
  • You can check your Bioconductor installation with
BiocManager::valid()
  • Each Bioconductor package has a landing page (e.g., http://bioconductor.org/packages/limma/) that contains relevant information, including installation instructions, vignettes and the reference manual: