Bioconductor
Stable release
3.14 / 27 October 2021; 5 months ago (2021-10-27)
Operating systemLinux, macOS, Windows
PlatformR programming language
TypeBioinformatics
LicenseArtistic License 2.0
Websitewww.bioconductor.org

Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology.

Bioconductor is based primarily on the statistical R programming language, but does contain contributions in other programming languages. It has two releases each year that follow the semiannual releases of R. At any one time there is a release version, which corresponds to the released version of R, and a development version, which corresponds to the development version of R. Most users will find the release version appropriate for their needs. In addition there are many genome annotation packages available that are mainly, but not solely, oriented towards different types of microarrays.

While computational methods continue to be developed to interpret biological data, the Bioconductor project is an open source software repository that hosts a wide range of statistical tools developed in the R programming environment. Utilizing a rich array of statistical and graphical features in R, many Bioconductor packages have been developed to meet various data analysis needs. The use of these packages provides a basic understanding of the R programming / command language. As a result, R and Bioconductor packages, which have a strong computing background, are used by most biologists who will benefit significantly from their ability to analyze datasets. All these results provide biologists with easy access to the analysis of genomic data without requiring programming expertise.

The project was started in the Fall of 2001 and is overseen by the Bioconductor core team, based primarily at the Fred Hutchinson Cancer Research Center, with other members coming from international institutions.

Packages

Most Bioconductor components are distributed as R packages, which are add-on modules for R. Initially most of the Bioconductor software packages focused on the analysis of single channel Affymetrix and two or more channel cDNA/Oligo microarrays. As the project has matured, the functional scope of the software packages broadened to include the analysis of all types of genomic data, such as SAGE, sequence, or SNP data.

Goals

The broad goals of the projects are to:

Main features

Milestones

Each release of Bioconductor is developed to work best with a chosen version of R.[1] In addition to bugfixes and updates, a new release typically adds packages. The table below maps a Bioconductor release to a R version and shows the number of available Bioconductor software packages for that release.

Version Release date Package count R dependency
3.14 27 Oct 2021 2083 R 4.1
3.13 20 May 2021 2042 R 4.1
3.11 28 Apr 2020 1903 R 4.0
3.10 30 Oct 2019 1823 R 3.6
3.8 31 Oct 2018 1649 R 3.5
3.6 31 Oct 2017 1473 R 3.4
3.4 18 Oct 2016 1296 R 3.3
3.2 14 Oct 2015 1104 R 3.2
3.0 14 Oct 2014 934 R 3.1
2.13 15 Oct 2013 749 R 3.0
2.11 3 Oct 2012 610 R 2.15
2.9 1 Nov 2011 517 R 2.14
2.8 14 Apr 2011 466 R 2.13
2.7 18 Nov 2010 418 R 2.12
2.6 23 Apr 2010 389 R 2.11
2.5 28 Oct 2009 352 R 2.10
2.4 21 Apr 2009 320 R 2.9
2.3 22 Oct 2008 294 R 2.8
2.2 1 May 2008 260 R 2.7
2.1 8 Oct 2007 233 R 2.6
2.0 26 Apr 2007 214 R 2.5
1.9 4 Oct 2006 188 R 2.4
1.8 27 Apr 2006 172 R 2.3
1.7 14 Oct 2005 141 R 2.2
1.6 18 May 2005 123 R 2.1
1.5 25 Oct 2004 100 R 2.0
1.4 17 May 2004 81 R 1.9
1.3 30 Oct 2003 49 R 1.8
1.2 29 May 2003 30 R 1.7
1.1 19 Oct 2002 20 R 1.6
1.0 1 May 2002 15 R 1.5

Resources

See also

References


  1. ^ "Bioconductor – Release Announcements". bioconductor.org. Bioconductor. Retrieved 28 May 2019.