What is Bioconductor?
- The project was started in 2001 (back then, mostly focused on microarray data)
- Currently (release 3.10) hosts:
- 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
- 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
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:
- You can check your Bioconductor installation with
- 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: