Here is a list of the advantages of having Bioconductor for the bioinformatic community:
- Outreach: You have a repository for the field, in that language.
Some packages related to bioinformatics (in R) are distributed through personal repositories, CRAN, github, bitbucket, sourceforge, but they are less used and harder to find.
There are such efforts in other languages too: Biopython, Bioperl, Biojava, ...
Also is harder to find the repositories related to a subject in CRAN, you don't have the BiocViews, the equivalent is optional and not usually filled, which is quite useful when looking for a method.
- Quality: In Bioconductor each package is tested in Linux, Windows, and iOS, to make sure it works in all major operative systems (with all the dependencies).
In some rare cases like this one, a packages is not supported for certain platform, but you can known it by checking the build report.
You are required to provide a vignette and examples in every exported element (and the vignette, examples and tests should pass). You are required to be able to install the package with stricter quality than CRAN, because there is a manual review (They pointed out a comment in one of my functions!).
They also provide docker images of the base packages. You don't need to install the latest R version to use the Bioconductor! But developers do so (at least when checked by Bioconductor servers) to ensure that the package will keep working in next R release.
- Reusing: Bioconductor provides the basic elements to a big number of applications.
For example the summarizedExperiment class is provided so that any package that needs a similar object can (should) use it. Or GSEABase is the base package to deal with GSEA enrichment analysis, providing functions, methods and classes for gene sets, and collections, making easier for anyone to create their own GSE analysis.
It is easier to build upon the work of others if you know you are following the same quality standards.
- Support: To support Q&A is mandatory, the package maintainer must be registered in the webpage.
While in CRAN usually the support is given by each package in its own way, in Bioconductor you can directly reach the maintainer and the users by posting in the same central place.