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Bioconductor
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<h2 id="packages">Packages</h2> <p>Most Bioconductor components are distributed as <a href="/facts/R_packages/etUNSDLc">R packages</a>, which are add-on modules for R. Initially most of the Bioconductor software packages focused on the analysis of single channel <a href="/facts/Affymetrix/SbQJUYzU">Affymetrix</a> and two or more channel <a href="/facts/Complementary_DNA/P2nWeY4T">cDNA</a>/<a href="/facts/Oligonucleotide/Gc99fPnC">Oligo</a> 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, <a href="/facts/Sequence_(biology)/JKT2Hh9s">sequence</a>, or <a href="/facts/Single_nucleotide_polymorphism/Qy5Y2wom">SNP</a> data. </p> <h2 id="goals">Goals</h2> <p>The broad goals of the projects are to: </p> <ul><li>Provide widespread access to a broad range of powerful <a href="/facts/Statistics/DNPsKGYU">statistical</a> and <a href="/facts/Statistical_graphics/SAo9EjFx">graphical</a> methods for the analysis of genomic data.</li> <li>Facilitate the inclusion of <a href="/facts/Genome_annotation/HY6IuzMT">biological metadata</a> in the analysis of genomic data, e.g. literature data from <a href="/facts/PubMed/JlHAvMHt">PubMed</a>, annotation data from LocusLink/<a href="/facts/Entrez/1b3UvdGY">Entrez</a>.</li> <li>Provide a common <a href="/facts/Computing_platform/DmKwp5Bk">software platform</a> that enables the rapid <a href="/facts/Software_development/UUfsAaYY">development</a> and <a href="/facts/Software_deployment/9yMpwGTu">deployment</a> of <a href="/facts/Plug-in_(computing)/351Du3Wu">plug-able</a>, <a href="/facts/Scalability/jh7JomPa">scalable</a>, and <a href="/facts/Interoperability/7WgqUbXU">interoperable</a> software.</li> <li>Further scientific understanding by producing high-quality <a href="/facts/Tutorial/PrsIwPo4">documentation and reproducible research</a>.</li> <li>Train researchers on computational and statistical methods for the analysis of genomic data.</li></ul> <h2 id="main-features">Main features</h2> <ul><li><a href="/facts/Tutorial/PrsIwPo4">Documentation and reproducible research</a>. 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.</li> <li><a href="/facts/Statistics/DNPsKGYU">Statistical and graphical methods</a>. The Bioconductor project aims to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data. Analysis packages are available for: pre-processing <a href="/facts/Affymetrix/SbQJUYzU">Affymetrix</a> and <a href="/facts/Illumina_(company)/0nofTkVp">Illumina</a>, <a href="/facts/Complementary_DNA/P2nWeY4T">cDNA</a> array data; identifying <a href="/facts/Expression_profiling/BbyYB94G">differentially expressed genes</a>; graph theoretical analyses; plotting genomic data. In addition, the R package system itself provides implementations for a broad range of state-of-the-art <a href="/facts/Statistics/DNPsKGYU">statistical</a> and <a href="/facts/Statistical_graphics/SAo9EjFx">graphical</a> techniques, including <a href="/facts/Linear_regression/5n998IhK">linear</a> and <a href="/facts/Nonlinear_regression/8mMuJSe8">non-linear</a> modeling, <a href="/facts/Cluster_analysis/HUeDnWPt">cluster analysis</a>, <a href="/facts/Prediction/0w4XXB33">prediction</a>, <a href="/facts/Resampling_(statistics)/yq6LXqnX">resampling</a>, <a href="/facts/Survival_analysis/q8w13cjl">survival analysis</a>, and <a href="/facts/Time_series/fSXPR817">time series</a> analysis.</li> <li><a href="/facts/Genome_annotation/HY6IuzMT">Genome annotation</a>. The Bioconductor project provides software for associating microarray and other genomic data in real time to biological metadata from web databases such as <a href="/facts/GenBank/XyMcrktE">GenBank</a>, LocusLink and <a href="/facts/PubMed/JlHAvMHt">PubMed</a> (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 <a href="/facts/GenBank/XyMcrktE">GenBank</a>, the <a href="/facts/Gene_Ontology/Grmg6Q8k">Gene Ontology Consortium</a>, LocusLink, <a href="/facts/UniGene/mzaEcNvL">UniGene</a>, the <a href="/facts/Human_Genome_Project/eQDHgHTP">UCSC Human Genome Project</a> and others with the AnnotationDbi package. Data packages are distributed to provide mappings between different probe identifiers (e.g. Affy IDs, LocusLink, <a href="/facts/PubMed/JlHAvMHt">PubMed</a>). Customized annotation libraries can also be assembled.This project also contain several functions for genomic analysis and phylogenetic (e.g. <a href="http://bioconductor.org/packages/release/bioc/html/ggtree.html">ggtree</a>, <a href="https://cran.r-project.org/web/packages/phytools/index.html">phytools</a> packages ..).</li> <li><a href="/facts/Open-source_software/HzTaB8E9">Open source</a>. The Bioconductor project has a commitment to full open source discipline, with distribution via a <a href="/facts/SourceForge.net/lxYAgUAX">SourceForge.net</a>-like platform. All contributions are expected to exist under an <a href="/facts/Open_source_license/FlFTwHmd">open source license</a> such as <a href="/facts/Artistic_License/9vHBm47P">Artistic 2.0</a>, <a href="/facts/GNU_General_Public_License/S75KhLSX">GPL2</a>, or <a href="/facts/Berkeley_Software_Distribution/XQKcURrh">BSD</a>. There are many different reasons why open-source software is beneficial to the analysis of microarray data and to <a href="/facts/Computational_biology/GxgNfwcX">computational biology</a> in general. The reasons include: <ul><li>To provide full access to <a href="/facts/Algorithm/fnl5NmRt">algorithms</a> and their implementation</li> <li>To facilitate software improvements through <a href="/facts/Software_bug/I1uSXySv">bug fixing</a> and <a href="/facts/Plug-in_(computing)/351Du3Wu">plug-ins</a></li> <li>To encourage good <a href="/facts/Computational_statistics/noW2SBX8">scientific computing and statistical practice</a> by providing appropriate tools and instruction</li> <li>To provide a <a href="/facts/Application_software/YQuj7Kog">workbench of tools</a> that allow researchers to explore and expand the methods used to analyze biological data</li> <li>To ensure that the international <a href="/facts/Scientific_community/0YIPcVzE">scientific community</a> is the owner of the <a href="/facts/Programming_tool/wWaFqCFw">software tools</a> needed to carry out research</li> <li>To lead and encourage commercial support and development of those tools that are successful</li> <li>To promote <a href="/facts/Reproducibility/yh5pawMj">reproducible research</a> by providing open and accessible tools with which to carry out that research (reproducible research is distinct from independent verification)</li></ul></li> <li><a href="/facts/Open_source_software_development/tAMqzWxB">Open development</a>. <a href="/facts/End-user_(computer_science)/7IM9qu7N">Users</a> are encouraged to become <a href="/facts/Software_developer/WGTS1Jv9">developers</a>, either by contributing Bioconductor compliant packages or documentation. Additionally Bioconductor provides a mechanism for linking together different groups with <a href="/facts/Goal_setting/1IvADhEv">common goals</a> to foster <a href="/facts/Collaboration/8rkNh7hP">collaboration</a> on software, possibly at the level of shared development.</li></ul> <h2 id="milestones">Milestones</h2> <p>Each release of Bioconductor is developed to work best with a chosen version of R.<a class="footnote-ref" id="fnref:1" href="#fn:1"><sup>1</sup></a> 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. </p> <table><tbody><tr><th>Version</th><th>Release date</th><th>Package count</th><th>R dependency</th></tr><tr><td>3.20</td><td>30 Oct 2024</td><td>2289</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 4.4</a></td></tr><tr><td>3.19</td><td>1 May 2024</td><td>2300</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 4.4</a></td></tr><tr><td>3.18</td><td>25 Oct 2023</td><td>2266</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 4.3</a></td></tr><tr><td>3.16</td><td>2 Nov 2022</td><td>2183</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 4.2</a></td></tr><tr><td>3.14</td><td>27 Oct 2021</td><td>2083</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 4.1</a></td></tr><tr><td>3.11</td><td>28 Apr 2020</td><td>1903</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 4.0</a></td></tr><tr><td>3.10</td><td>30 Oct 2019</td><td>1823</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 3.6</a></td></tr><tr><td>3.8</td><td>31 Oct 2018</td><td>1649</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 3.5</a></td></tr><tr><td>3.6</td><td>31 Oct 2017</td><td>1473</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 3.4</a></td></tr><tr><td>3.4</td><td>18 Oct 2016</td><td>1296</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 3.3</a></td></tr><tr><td>3.2</td><td>14 Oct 2015</td><td>1104</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 3.2</a></td></tr><tr><td>3.0</td><td>14 Oct 2014</td><td>934</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 3.1</a></td></tr><tr><td>2.13</td><td>15 Oct 2013</td><td>749</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 3.0</a></td></tr><tr><td>2.11</td><td>3 Oct 2012</td><td>610</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.15</a></td></tr><tr><td>2.9</td><td>1 Nov 2011</td><td>517</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.14</a></td></tr><tr><td>2.8</td><td>14 Apr 2011</td><td>466</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.13</a></td></tr><tr><td>2.7</td><td>18 Nov 2010</td><td>418</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.12</a></td></tr><tr><td>2.6</td><td>23 Apr 2010</td><td>389</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.11</a></td></tr><tr><td>2.5</td><td>28 Oct 2009</td><td>352</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.10</a></td></tr><tr><td>2.4</td><td>21 Apr 2009</td><td>320</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.9</a></td></tr><tr><td>2.3</td><td>22 Oct 2008</td><td>294</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.8</a></td></tr><tr><td>2.2</td><td>1 May 2008</td><td>260</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.7</a></td></tr><tr><td>2.1</td><td>8 Oct 2007</td><td>233</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.6</a></td></tr><tr><td>2.0</td><td>26 Apr 2007</td><td>214</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.5</a></td></tr><tr><td>1.9</td><td>4 Oct 2006</td><td>188</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.4</a></td></tr><tr><td>1.8</td><td>27 Apr 2006</td><td>172</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.3</a></td></tr><tr><td>1.7</td><td>14 Oct 2005</td><td>141</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.2</a></td></tr><tr><td>1.6</td><td>18 May 2005</td><td>123</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.1</a></td></tr><tr><td>1.5</td><td>25 Oct 2004</td><td>100</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 2.0</a></td></tr><tr><td>1.4</td><td>17 May 2004</td><td>81</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 1.9</a></td></tr><tr><td>1.3</td><td>30 Oct 2003</td><td>49</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 1.8</a></td></tr><tr><td>1.2</td><td>29 May 2003</td><td>30</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 1.7</a></td></tr><tr><td>1.1</td><td>19 Oct 2002</td><td>20</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 1.6</a></td></tr><tr><td>1.0</td><td>1 May 2002</td><td>15</td><td><a href="/facts/R_(programming_language)/LSrkr8K8">R 1.5</a></td></tr></tbody></table> <h2 id="resources">Resources</h2> <ul><li><a href="/facts/Robert_Gentleman_(statistician)/8qM9fEBU">Gentleman, R.</a>; Carey, V.; <a href="/facts/Wolfgang_Huber_(scientist)/BvIg79mx">Huber, W.</a>; <a href="/facts/Rafael_Irizarry_(scientist)/1pfupHaX">Irizarry, R.</a>; <a href="/facts/Sandrine_Dudoit/H5e7F9kz">Dudoit, S.</a> (2005). <i>Bioinformatics and Computational Biology Solutions Using R and Bioconductor</i>. Springer. <a href="/facts/ISBN_(identifier)/15AdSPa9">ISBN</a> 978-0-387-25146-2.</li> <li><a href="/facts/Robert_Gentleman_(statistician)/8qM9fEBU">Gentleman, R.</a> (2008). <a href="https://books.google.com/books?id=34Y6WjJy8zEC"><i>R Programming for Bioinformatics</i></a>. Chapman & Hall/CRC. <a href="/facts/ISBN_(identifier)/15AdSPa9">ISBN</a> 978-1-4200-6367-7.</li> <li>Hahne, F.; <a href="/facts/Wolfgang_Huber_(scientist)/BvIg79mx">Huber, W.</a>; <a href="/facts/Robert_Gentleman_(statistician)/8qM9fEBU">Gentleman, R.</a>; Falcon, S. (2008). <a href="https://books.google.com/books?id=F3tAehmRHSwC"><i>Bioconductor Case Studies</i></a>. Springer. <a href="/facts/ISBN_(identifier)/15AdSPa9">ISBN</a> 978-0-387-77239-4.</li> <li><a href="/facts/Robert_Gentleman_(statistician)/8qM9fEBU">Gentleman, Robert C.</a>; Carey, Vincent J.; Bates, Douglas M.; Bolstad, Ben; <a href="/facts/Marcel_Dettling/vm7GTUGW">Dettling, Marcel</a>; <a href="/facts/Sandrine_Dudoit/H5e7F9kz">Dudoit, Sandrine</a>; Ellis, Byron; Gautier, Laurent; Ge, Yongchao; Gentry, Jeff; Hornik, Kurt; Hothorn, Torsten; <a href="/facts/Wolfgang_Huber_(scientist)/BvIg79mx">Huber, Wolfgang</a>; Iacus, Stefano; <a href="/facts/Rafael_Irizarry_(scientist)/1pfupHaX">Irizarry, Rafael</a>; Leisch, Friedrich; Li, Cheng; Maechler, Martin; Rossini, Anthony J.; Sawitzki, Gunther; Smith, Colin; Smyth, Gordon; <a href="/facts/Luke_Tierney/C9VLnW14">Tierney, Luke</a>; <a href="/facts/Jean_Yang/UR3sYPaP">Yang, Jean Y. H.</a>; Zhang, Jianhua (2004). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC545600">"Bioconductor: open software development for computational biology and bioinformatics"</a>. <i><a href="/facts/Genome_Biology/Rc5drvSo">Genome Biology</a></i>. 5 (10): R80. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1186%2Fgb-2004-5-10-r80">10.1186/gb-2004-5-10-r80</a>. <a href="/facts/PMC_(identifier)/dX1zMt71">PMC</a> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC545600">545600</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/15461798">15461798</a>.</li></ul> <h2 id="see-also">See also</h2> <ul> <li>Free and open-source software portal</li><li>Biology portal</li></ul> <ul><li><a href="/facts/Computational_biology/GxgNfwcX">Computational biology</a></li> <li><a href="/facts/Bioinformatics/D5x2L8ee">Bioinformatics</a></li> <li><a href="/facts/List_of_open_source_bioinformatics_software/ED99kaN9">List of open source bioinformatics software</a></li> <li><a href="/facts/List_of_sequence_alignment_software/6AJKAI0p">List of sequence alignment software</a></li> <li><a href="/facts/R_(programming_language)/LSrkr8K8">R (programming language)</a></li> <li><a href="/facts/DNA_microarray/hofkMvou">DNA microarray</a></li> <li><a href="/facts/Affymetrix/SbQJUYzU">Affymetrix</a>, a microarray technology platform</li></ul> <h2 id="external-links">External links</h2> <ul><li><a href="//www.bioconductor.org">Official website</a></li> <li><a href="http://www.r-project.org">The R Project</a> <a href="/facts/GNU/HlAKKBdt">GNU</a> R is a programming language for statistical computing.</li> <li><a href="http://www.bioconductor.org/about/release-announcements/">Bioconductor Releases</a></li> <li>The community of the <a href="/facts/Debian/cBd93qfJ">Debian GNU/Linux</a> distribution strives towards an <a href="http://wiki.debian.org/AliothPkgBioc">automated building of BioConductor packages</a> <a href="https://web.archive.org/web/20070811135011/http://wiki.debian.org/AliothPkgBioc">Archived</a> 2007-08-11 at the <a href="/facts/Wayback_Machine/nmQ3a6JC">Wayback Machine</a> for their distribution. <a href="https://web.archive.org/web/20051124175716/http://bioknoppix.hpcf.upr.edu/">BioKnoppix</a> and <a href="http://dirk.eddelbuettel.com/quantian.html">Quantian</a> are projects extending <a href="/facts/Knoppix/BkrEUxHC">Knoppix</a> that have contributed bootable <a href="/facts/Debian/cBd93qfJ">Debian GNU/Linux</a> CDs providing BioConductor installations.</li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>"Bioconductor – Release Announcements". bioconductor.org. Bioconductor. Retrieved 28 May 2019. <a href="https://bioconductor.org/about/release-announcements/" target="_blank">https://bioconductor.org/about/release-announcements/</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> </ol>