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We are dedicated to building a diverse, collaborative, and welcoming community of developers and data scientists.</p> <p><a href="scientific-advisory-board/">Scientific</a>, <a href="technical-advisory-board/">Technical</a> and <a href="community-advisory-board/">Community</a> Advisory Boards provide project oversight.</p> <h2 id="release-and-core-development">Release and Core Development</h2> <p>The Bioconductor <a href="/packages/release/">release version</a> is updated twice each year, and is appropriate for most users. There is also a <a href="/packages/devel/">development version</a>, to which new features and packages are added prior to incorporation in the release. A large number of <a href="/packages/release/data/annotation">meta-data packages</a> provide pathway, organism, microarray and other annotations.</p> <p>The Bioconductorproject started in 2001 and is overseen by a <a href="/about/core-team/">core team</a>. A <a href="community-advisory-board/">Community Advisory Board</a> and a <a href="technical-advisory-board/">Technical Advisory Board</a> of key participants meets monthly to support the Bioconductor mission by coordinating training and outreach activities, developing strategies to ensure long-term technical suitability of core infrastructure, and to identify and enable funding strategies for long-term viability. A <a href="scientific-advisory-board/">Scientific Advisory Board</a> including external experts provides annual guidance and accountability.</p> <p>Key citations to the project include Huber et al., 2015 <a href="http://www.nature.com/nmeth/journal/v12/n2/abs/nmeth.3252.html">Nature Methods 12:115-121</a> and Gentleman et al., 2004 <a href="https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2004-5-10-r80.pdf">Genome Biology 5:R80</a></p> <div class="about-join"> <section class="gradient-border join container"> <div class="gradient-border-inner section-block"> <input type="radio" class="tabs-join-radio" name="tabs-join" id="join-tab1" aria-label="View scientists join information" checked="" /> <div class="join-row"> <div class="join-content"> <h2>Start Using Bioconductor</h2> <p class="text-large"> Join our ever-growing community and discover how Bioconductor can <mark class="text-gradient format-bold">improve your pipeline</mark> </p> <div class="join-buttons"> <a class="brand-border-button" href="/install/"> <span class="span-brand format-bold"> Get started <svg xmlns="http://www.w3.org/2000/svg" width="14" height="15" viewBox="0 0 14 15" fill="none"> <path d="M5.25 3.66665L9.33333 7.74998L5.25 11.8333" stroke="#3792AD" stroke-width="2.2" stroke-linecap="round" stroke-linejoin="round" /> </svg> </span> </a> <a class="learn-more format-bold" href="/help/">Learn more about using Bioconductor</a> </div> </div> <div class="join-img-div"> <img src="/images/icons/Join-Data-Scientists.png" class="join-img" alt="Image depicting boxes and lines" /> </div> </div> <input type="radio" class="tabs-join-radio" name="tabs-join" id="join-tab2" aria-label="View developers join information" /> <div class="join-row"> <div class="join-content"> <h2>Contribute to Bioconductor</h2> <p class="text-large"> Bioconductor is open source! Join our community of developers and <mark class="text-gradient format-bold">develop your package</mark> </p> <div class="join-buttons"> <a class="brand-border-button" href="/developers/"> <span class="span-brand format-bold"> Developers' Resources <svg xmlns="http://www.w3.org/2000/svg" width="14" height="15" viewBox="0 0 14 15" fill="none"> <path d="M5.25 3.66665L9.33333 7.74998L5.25 11.8333" stroke="#3792AD" stroke-width="2.2" stroke-linecap="round" stroke-linejoin="round" /> </svg> </span> </a> <a class="learn-more format-bold" href="/help/">Learn more about using Bioconductor</a> </div> </div> <div class="join-img-div"> <img src="/images/icons/Join-Developers.png" class="join-img" alt="Image depicting Bioconductor hexagon logos" /> </div> </div> </div> </section> </div> <h2 id="bioconductor-packages">Bioconductor Packages</h2> <p>Most Bioconductor components are distributed as <a href="http://cran.r-project.org/doc/FAQ/R-FAQ.html#R-Add_002dOn-Packages">R packages</a>. The functional scope of <a href="/packages/release/">Bioconductor packages</a> includes the analysis of DNA microarray, sequence, flow, SNP, and other genetic or genomic data.</p> <h2 id="project-goals">Project Goals</h2> <p>The broad goals of the Bioconductor project are:</p> <ul> <li>To provide widespread access to a broad range of powerful statistical and graphical methods for the analysis of genomic data.</li> <li>To facilitate the inclusion of biological metadata in the analysis of genomic data, e.g. literature data from PubMed, annotation data from Entrez genes.</li> <li>To provide a common software platform that enables the rapid development and deployment of extensible, scalable, and interoperable software.</li> <li>To further scientific understanding by producing high-quality <a href="/help/package-vignettes/">documentation</a> and reproducible research.</li> <li>To <a href="https://training.bioconductor.org/">train</a> researchers on computational and statistical methods for the analysis of genomic data.</li> </ul> <h2 id="main-project-features">Main Project Features</h2> <p>The R project for Statistical Computing. Using <a href="http://www.r-project.org">R</a> provides a broad range of advantages to the Bioconductor project, including:</p> <ul> <li>A high-level interpreted language to easily and quickly prototype new computational methods.</li> <li>A well established system for packaging together software with documentation.</li> <li>An object-oriented framework for addressing the diversity and complexity of computational biology and bioinformatics problems.</li> <li>Access to on-line computational biology and bioinformatics data.</li> <li>Support for rich statistical simulation and modeling activities.</li> <li>Cutting edge data and model visualization capabilities.</li> <li>Active development by a dedicated team of researchers with a strong commitment to good documentation and software design.</li> </ul> <h4 id="documentation-and-reproducible-research">Documentation and reproducible research</h4> <p>Each <a href="/packages/release/">Bioconductor package</a> contains one or more <a href="/help/package-vignettes/">vignettes</a>, documents that provide a textual, task-oriented description of the package鈥檚 functionality. Vignettes come in several forms. Many are 鈥淗owTo鈥漵 that demonstrate how a particular task can be accomplished with that package鈥檚 software. Others provide a more thorough overview of the package or discuss general issues related to the package.</p> <h4 id="statistical-and-graphical-methods">Statistical and graphical methods</h4> <p>The Bioconductor project provides access to powerful statistical and graphical methods for the analysis of genomic data. <a href="/packages/release/bioc/">Analysis packages</a> address <a href="/packages/release/workflows/">workflows</a> for analysis of oligonucleotide arrays, sequence analysis, flow cytometry. and other high-throughput genomic data. The <a href="http://cran.r-project.org/doc/FAQ/R-FAQ.html#R-Add_002dOn-Packages">R package system</a> 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-series analysis.</p> <h4 id="annotation">Annotation</h4> <p>The Bioconductor project provides software for associating microarray and other genomic data in real time with biological metadata from web databases such as GenBank, Entrez genes and PubMed (<a href="/packages/release/bioc/html/annotate.html">annotate</a> package). Functions are also provided for incorporating the results of statistical analysis in HTML reports with links to annotation web resources. Software tools are available for assembling and processing genomic annotation data, from databases such as GenBank, the Gene Ontology Consortium, Entrez genes, UniGene, the UCSC Human Genome Project (<a href="/packages/release/bioc/html/AnnotationDbi.html">AnnotationDbi</a> package). <a href="/packages/release/data/annotation/">Annotation data packages</a> are distributed to provide mappings between different probe identifiers (e.g. Affy IDs, Entrez genes, PubMed). Customized annotation libraries can also be assembled.</p> <h4 id="bioconductor-short-courses">Bioconductor short courses</h4> <p>The Bioconductor project has developed a program of <a href="/help/course-materials/">short courses</a> on software and statistical methods for the analysis of genomic data. Courses have been given for audiences with backgrounds in either biology or statistics. All <a href="/help/course-materials/">course materials</a> (lectures and computer labs) are available on this site. There is also a <a href="https://training.bioconductor.org/">Bioconductor teaching committee</a> to consolidate Bioconductor-focused training materials and establish a community of Bioconductor trainers.</p> <h4 id="open-source">Open source</h4> <p>The Bioconductor project has a commitment to full open source discipline, with distribution via a public git (version control) server. Almost all contributions exist under an open source license. There are many different reasons why open source software is beneficial to the analysis of microarray data and to computational biology in general. The reasons include:</p> <ul> <li>To provide full access to algorithms and their implementation</li> <li>To facilitate software improvements through bug fixing and software extension</li> <li>To encourage good scientific computing and statistical practice by providing appropriate tools and instruction</li> <li>To provide a workbench of tools that allow researchers to explore and expand the methods used to analyze biological data</li> <li>To ensure that the international scientific community is the owner of the software tools 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 reproducible research by providing open and accessible tools with which to carry out that research (reproducible research is distinct from independent verification)</li> </ul> <h4 id="open-development">Open development</h4> <p>Users are encouraged to become developers, either by contributing <a href="http://contributions.bioconductor.org/develop-overview.html">Bioconductor compliant packages</a> or documentation. Additionally Bioconductor provides a mechanism for linking together different groups with common goals to foster collaboration on software, often at the level of shared development.</p> <h2 id="quick-statistics">Quick Statistics</h2> <p class="text-large">A selection of statistics about the project.</p> <div> <div class="gradient-border learn container"> <div class="section-block" style="margin: 2px;"> <h2>Quick Stats</h2> <p>Last updated <abbr class="timeago" title="2023-12-21">"2023-12-18"</abbr></p> <p class="text-large">3691 total <mark class="text-gradient format-bold">Release Packages</mark></p> <p class="text-large">45546715 distinct <mark class="text-gradient format-bold">Software Downloads in 2023</mark></p> <p class="text-large">18999 active <mark class="text-gradient format-bold">Support Site Members</mark> in the last year</p> <p class="text-large">550 active <mark class="text-gradient format-bold">Slack Members</mark></p> <p class="text-large">122000 <mark class="text-gradient format-bold">Google Scholar</mark> results</p> <p>Request updated statistics from: <a href="mailto:maintainer@bioconductor.org">maintainer@bioconductor.org</a></p> </div> </div> </div> <h2 id="code-of-conduct">Code of Conduct</h2> <p>Please refer to the <a href="code-of-conduct/">Bioconductor Code of Conduct</a></p> <h2 id="contact">Contact</h2> <p>Please reach out to <a href="mailto:bioconductorcoreteam@gmail.com">bioconductorcoreteam@gmail.com</a></p> <p><img src="/images/icons/BioconductorSticker1.png" alt="Bioconductor sticker" /></p> </section> </main> <footer> <div class="footer-container"> <div class="link-container"> <div class="link-container-inner"> <nav> <a href="/about/index.html"><h3>About</h3></a> <a href="/about/annual-reports/">Annual Reports</a> <a href="/about/collaborations/">Collaborations</a> <a href="/about/core-team/">Core Team</a> <a href="/about/mirrors/">Mirrors</a> <a href="/dashboard/">Dashboard</a> <a href="/about/">Project Details</a> <a href="/about/code-of-conduct/">Code of Conduct</a> </nav> <nav> <a href="/developers/index.html"><h3>Developers</h3></a> <a href="https://contributions.bioconductor.org/develop-overview.html">Package Guidelines</a> <a href="https://contributions.bioconductor.org/submission-overview.html">Package Submission</a> <a href="/developers/release-schedule/">Release Schedule</a> <a href="/about/release-announcements/">Release Announcements</a> <a href="https://contributions.bioconductor.org/git-version-control.html">Source Control</a> <a href="https://code.bioconductor.org/">Browsable Code Base</a> <a href="/checkResults/">Build Reports</a> </nav> </div> <div class="link-container-inner"> <nav> <a href="/help/index.html"><h3>Learn</h3></a> <a href="https://training.bioconductor.org/">Education and Training</a> <a href="/help/bioconductor-books/">Bioconductor Books</a> <a href="/help/package-vignettes/">Package Vignettes</a> <a href="/packages/release/workflows/">Workflows</a> <a href="/help/publications/">Publications</a> <a href="/help/community/">Community Resources</a> <a href="/help/support/">Get Help</a> </nav> <nav> <a href="/install/index.html"><h3>Get started</h3></a> <a href="/install/index.html#install-R">Install R</a> <a href="/install/index.html#find-bioconductor-packages">Find Bioconductor Packages</a> <a href="/install/index.html#install-bioconductor-packages">Install Bioconductor Packages</a> <a href="/install/index.html#update-bioconductor-packages">Update Bioconductor Packages</a> <a href="/help/docker/">Docker Images</a> <a href="https://anvil.bioconductor.org/">Bioconductor in AnVIL</a> <a href="/packages/release/BiocViews.html#___Software">Bioconductor Packages</a> </nav> </div> </div> <div class="logo-contact-container"> <div class="copyright"> <p> Contact us: <a class="text-underline" href="https://support.bioconductor.org/">support.bioconductor.org</a><br/> Copyright © 2003 - 2024 Bioconductor </p> </div> <div class="socials-logo-container"> <div class="socials"> <a href="https://slack.bioconductor.org/" target="_blank"><img alt="Slack Logo" src="/images/icons/slack.png" /></a> <a href="https://www.youtube.com/user/bioconductor" target="_blank"><img alt="YouTube Logo" src="/images/icons/svgs/youtube.svg" /></a> <a href="https://www.linkedin.com/company/bioconductor/" target="_blank"><img alt="LinkedIn Logo" src="/images/icons/svgs/linkedin.svg" /></a> <a href="https://bsky.app/profile/bioconductor.bsky.social" target="_blank"><img alt="Bluesky Logo" src="/images/icons/svgs/bluesky.svg" /></a> <a href="https://genomic.social/@bioconductor" target="_blank"><img alt="Mastodon Logo" src="/images/icons/svgs/mastodon.svg" /></a> <a href="https://blog.bioconductor.org/" target="_blank"><img alt="Blog Logo" src="/images/icons/svgs/arrow-circle-right-white.svg" /></a> </div> <img class="footer-logo" src="/images/logo/svg/BC-Logo-White.svg" alt="BioConductor Logo in White" /> </div> </div> </div> </footer> </body> </html>

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