Bioconductor
Stable release | 3.17
/ 26 April 2023 |
---|---|
R programming language | |
Type | Bioinformatics |
License | Artistic License 2.0 |
Website | www |
Bioconductor is a
Bioconductor is based primarily on the
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
Packages
Most Bioconductor components are distributed as
Goals
The broad goals of the projects are to:
- Provide widespread access to a broad range of powerful statistical and graphical methods for the analysis of genomic data.
- Facilitate the inclusion of .
- Provide a common software platform that enables the rapid development and deployment of plug-able, scalable, and interoperable software.
- Further scientific understanding by producing high-quality documentation and reproducible research.
- Train researchers on computational and statistical methods for the analysis of genomic data.
Main features
- Documentation and reproducible research. Each Bioconductor package contains at least one vignette, which is a document that provides a textual, task-oriented description of the package's functionality. These vignettes come in several forms. Many are simple "How-to"s that are designed to demonstrate how a particular task can be accomplished with that package's software. Others provide a more thorough overview of the package or might even discuss general issues related to the package. In the future, the Bioconductor project is looking towards providing vignettes that are not specifically tied to a package, but rather are demonstrating more complex concepts. As with all aspects of the Bioconductor project, users are encouraged to participate in this effort.
- differentially expressed genes; graph theoretical analyses; plotting genomic data. In addition, the R package system itself provides implementations for a broad range of state-of-the-art statistical and graphical techniques, including linear and non-linear modeling, cluster analysis, prediction, resampling, survival analysis, and time seriesanalysis.
- Genome annotation. The Bioconductor project provides software for associating microarray and other genomic data in real time to biological metadata from web databases such as GenBank, LocusLink and PubMed (annotate package). Functions are also provided for incorporating the results of statistical analysis in HTML reports with links to annotation WWW resources. Software tools are available for assembling and processing genomic annotation data, from databases such as GenBank, the Gene Ontology Consortium, LocusLink, UniGene, the UCSC Human Genome Project and others with the AnnotationDbi package. Data packages are distributed to provide mappings between different probe identifiers (e.g. Affy IDs, LocusLink, PubMed). Customized annotation libraries can also be assembled.This project also contain several functions for genomic analysis and phylogenetic (e.g ggtree, phytoolspackages ..).
- open source license such as Artistic 2.0, GPL2, or BSD. There are many different reasons why open-source software is beneficial to the analysis of microarray data and to computational biologyin general. The reasons include:
- To provide full access to algorithms and their implementation
- To facilitate software improvements through bug fixing and plug-ins
- To encourage good scientific computing and statistical practice by providing appropriate tools and instruction
- To provide a workbench of tools that allow researchers to explore and expand the methods used to analyze biological data
- To ensure that the international scientific community is the owner of the software tools needed to carry out research
- To lead and encourage commercial support and development of those tools that are successful
- To promote reproducible research by providing open and accessible tools with which to carry out that research (reproducible research is distinct from independent verification)
- developers, either by contributing Bioconductor compliant packages or documentation. Additionally Bioconductor provides a mechanism for linking together different groups with common goals to foster collaborationon software, possibly at the level of shared development.
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 |
---|---|---|---|
3.17 | 26 Apr 2023 | 2230 | R 4.3 |
3.16 | 2 Nov 2022 | 2183 | R 4.2 |
3.14 | 27 Oct 2021 | 2083 | 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
- ISBN 978-0-387-25146-2.
- ISBN 978-1-4200-6367-7.
- Hahne, F.; ISBN 978-0-387-77239-4.
- PMID 15461798.
See also
- Computational biology
- Bioinformatics
- List of open source bioinformatics software
- List of sequence alignment software
- R (programming language)
- DNA microarray
- Affymetrix, a microarray technology platform
References
- ^ "Bioconductor – Release Announcements". bioconductor.org. Bioconductor. Retrieved 28 May 2019.
External links
- Official website
- The R Project GNU R is a programming language for statistical computing.
- Bioconductor Releases
- The community of the Debian GNU/Linux distribution strives towards an automated building of BioConductor packages Archived 2007-08-11 at the Wayback Machine for their distribution. BioKnoppix and Quantian are projects extending Knoppix that have contributed bootable Debian GNU/Linux CDs providing BioConductor installations.