Bioconductor

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Bioconductor

Bioconductor logo rgb.jpg
Basic data

Maintainer Bioconductor Core Team
Publishing year 2001
Current  version 3.4
(October 18, 2016)
operating system Unixoide , macOS , Windows
programming language R u. a.
category Bioinformatics library
License Artistic License
www.bioconductor.org/

Bioconductor is a collection of packages ( program libraries ) which extends the statistical programming language R with extensions from bioinformatics , in particular the analysis of gene expression data . Bioconductor was founded in 2001 and is an open source project. The aim was to create a platform to make software developments more transparent, to reduce multiple work and to bundle statistical and graphical methods and models for genetic data and to encourage their collaboration.

Bioconductor now offers a repository from which over 1200 packages for R can be downloaded. One of the most important and oldest packages is Biobase , which has a data structure that is adapted to the requirements of genetic data, so that a dataset of experiments with microarrays ( assayData ) together with typical metadata ( metadata ) and descriptive information ( experimentData ) can be saved, which is why many other packages use it.

The version cycle and version numbers follow R.

literature

  • Robert C. Gentleman et al. a .: Bioconductor: open software development for computational biology and bioinformatics . In: G. Brent Hall, Michael G. Leahy (Eds.): Genome Biology . tape 5 , no. 10 , 2004, p. R80.1 – R80.16 ( online [accessed August 2, 2016]).
  • Sorin Drăghici: Statistics and Data Analysis for Microarrays Using R and Bioconductor . 2nd Edition. Chapman & Hall / CRC, Boca Raton 2011, ISBN 978-1-4398-0975-4 .
  • Florian Hahne, Wolfgang Huber, Robert Gentleman, Seth Falcon: Bioconductor Case Studies . Springer, New York 2008, ISBN 978-0-387-77239-4 ( material ).
  • Robert Gentleman et al: Bioinformatics and Computational Biology Solutions Using R and Bioconductor . Springer, New York 2005, ISBN 978-0-387-25146-2 ( material ).

Web links

Individual evidence

  1. ↑ Wolfgang Huber u. a .: Orchestrating high-throughput genomic analysis with Bioconductor . In: Nature Methods . tape 12 , no. 1 , January 29, 2015, p. 115–121 ( online [accessed March 12, 2017] R package ).