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for the devel version, see <a href="/packages/devel/bioc/html/GenomeInfoDb.html">GenomeInfoDb</a>.</p> <h2>Utilities for manipulating chromosome names, including modifying them to follow a particular naming style</h2> <div class="sidebar-box" id="badges-box"> <section class="badges"> <a href="#archives"> <img src="/shields/availability/release/GenomeInfoDb.svg" alt="Platform availability badge" title="Whether the package is available on all platforms; click for details." /> </a> <a href="http://bioconductor.org/packages/stats/bioc/GenomeInfoDb/"> <img src="/shields/downloads/release/GenomeInfoDb.svg" alt="Ranking badge" title="Ranking by number of downloads. A lower number means the package is downloaded more frequently. Determined within a package type (software, experiment, annotation, workflow) and uses the number of distinct IPs for the last 12 months." /> </a> <a href="https://support.bioconductor.org/tag/genomeinfodb"> <img src="/shields/posts/GenomeInfoDb.svg" alt="Support activity badge" title="Support site activity, last 6 months: answered posts / total posts." /> </a> <a href="#since"> <img src="/shields/years-in-bioc/GenomeInfoDb.svg" alt="Years in BioConductor badge" title="How long since the package was first in a released Bioconductor version (or is it in devel only)." /> </a> <a href="https://bioconductor.org/checkResults/release/bioc-LATEST/GenomeInfoDb/"> <img src="/shields/build/release/bioc/GenomeInfoDb.svg" alt="Build results badge" title="build results; click for full report" /> </a> <a href="https://bioconductor.org/checkResults/release/bioc-LATEST/GenomeInfoDb/"> <img src="/shields/lastcommit/release/bioc/GenomeInfoDb.svg" alt="Last commit badge" title="time since last commit. possible values: today, < 1 week, < 1 month, < 3 months, since release, before release" /> </a> <a href="#since"> <img src="/shields/dependencies/release/GenomeInfoDb.svg" alt="Dependency count badge" title="Number of recursive dependencies needed to install package." /> </a> </section> <p> DOI: <a title="DOI for use in publications, etc., will always redirect to current release version (or devel if package is not in release yet)." href="https://doi.org/doi:10.18129/B9.bioc.GenomeInfoDb" > 10.18129/B9.bioc.GenomeInfoDb </a> </p> </div> <p><br></p> <div class="package-info"> <p> <strong>Bioconductor version:</strong> Release (3.20) </p> <p> Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order. </p> <p> <strong>Author:</strong> Sonali Arora [aut], Martin Morgan [aut], Marc Carlson [aut], Herv茅 Pag猫s [aut, cre], Prisca Chidimma Maduka [ctb], Atuhurira Kirabo Kakopo [ctb], Haleema Khan [ctb] (vignette translation from Sweave to Rmarkdown / HTML), Emmanuel Chigozie Elendu [ctb] <p /> <p> <strong>Maintainer:</strong> Herv茅 Pag猫s <hpages.on.github at gmail.com> </p> <div id="bioc-citation-outer"> <strong>Citation (from within R, enter <code>citation("GenomeInfoDb")</code>):</strong> <div id="bioc-citation" class="bioc-citation"></div> </div> </div> <h3>Installation</h3> <p> To install this package, start R (version "4.4") and enter: </p> <pre><code> if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("GenomeInfoDb") </code></pre> <p> For older versions of R, please refer to the appropriate <a href="/about/release-announcements/">Bioconductor release</a>. </p> <h3>Documentation</h3> <p>To view documentation for the version of this package installed in your system, start R and enter:</p> <pre><code>browseVignettes("GenomeInfoDb")</code></pre> <table> <tr> <td>GenomeInfoDb: Introduction to GenomeInfoDb</td> <td> <a onClick="javascript: pageTracker._trackPageview('../vignettes/GenomeInfoDb/inst/doc/GenomeInfoDb.pdf'); " href="../vignettes/GenomeInfoDb/inst/doc/GenomeInfoDb.pdf">PDF</a> </td> <td> <a onClick="javascript: pageTracker._trackPageview('../vignettes/GenomeInfoDb/inst/doc/GenomeInfoDb.R'); " href="../vignettes/GenomeInfoDb/inst/doc/GenomeInfoDb.R">R Script</a> </td> </tr> <tr> <td>Submitting your organism to GenomeInfoDb</td> <td> <a href="../vignettes/GenomeInfoDb/inst/doc/Accept-organism-for-GenomeInfoDb.html">HTML</a> </td> <td> <a onClick="javascript: pageTracker._trackPageview('../vignettes/GenomeInfoDb/inst/doc/Accept-organism-for-GenomeInfoDb.R'); " href="../vignettes/GenomeInfoDb/inst/doc/Accept-organism-for-GenomeInfoDb.R">R Script</a> </td> </tr> <tr> <td>Reference Manual</td> <td> <a onClick="javascript: pageTracker._trackPageview('../manuals/GenomeInfoDb/man/GenomeInfoDb.pdf'); " href="../manuals/GenomeInfoDb/man/GenomeInfoDb.pdf">PDF</a> </td> </tr> <tr> <td>NEWS</td> <td> <a href="../news/GenomeInfoDb/NEWS">Text</a> </td> </tr> <tr> <td></td> <td> <a href="http://youtu.be/wdEjCYSXa7w">Video</a> </td> </tr> </table> <p> <div class="info-section-button-padding"> <a class="brand-border-button" href="https://support.bioconductor.org/tag/genomeinfodb"> <span class="span-brand format-bold"> Need some help? Ask on the Bioconductor Support site! <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> </div> </p> <h3 id="details">Details</h3> <table class="full-width"> <tr> <td>biocViews</td> <td><a href="../../BiocViews.html#___Annotation">Annotation</a>, <a href="../../BiocViews.html#___DataRepresentation">DataRepresentation</a>, <a href="../../BiocViews.html#___Genetics">Genetics</a>, <a href="../../BiocViews.html#___GenomeAnnotation">GenomeAnnotation</a>, <a href="../../BiocViews.html#___Software">Software</a></td> </tr> <tr> <td>Version</td> <td>1.42.0</td> </tr> <tr id="since"> <td>In Bioconductor since</td> <td>BioC 2.14 (R-3.1) (10.5 years)</td> </tr> <tr> <td>License</td> <td>Artistic-2.0</td> </tr> <tr> <td>Depends</td> <td>R (>= 4.0.0), methods, <a href="../../bioc/html/BiocGenerics.html">BiocGenerics</a>(>= 0.37.0), <a href="../../bioc/html/S4Vectors.html">S4Vectors</a>(>= 0.25.12), <a href="../../bioc/html/IRanges.html">IRanges</a>(>= 2.13.12)</td> </tr> <tr> <td>Imports</td> <td>stats, stats4, utils, <a href="../../bioc/html/UCSC.utils.html">UCSC.utils</a>, <a href="../../data/annotation/html/GenomeInfoDbData.html">GenomeInfoDbData</a></td> </tr> <tr> <td>System Requirements</td> <td></td> </tr> <tr> <td>URL</td> <td><a href="https://bioconductor.org/packages/GenomeInfoDb">https://bioconductor.org/packages/GenomeInfoDb</a> </td> </tr> <tr> <td>Bug Reports</td> <td><a href="https://github.com/Bioconductor/GenomeInfoDb/issues">https://github.com/Bioconductor/GenomeInfoDb/issues</a> </td> </tr> </table> <details> <summary class="package-details">See More</summary> <table class="full-width"> <tr> <td>Suggests</td> <td><a class="cran_package" href="http://cran.rstudio.com/web/packages/R.utils/index.html">R.utils</a>, <a 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href="../../data/annotation/html/SNPlocs.Hsapiens.dbSNP144.GRCh38.html">SNPlocs.Hsapiens.dbSNP144.GRCh38</a>, <a href="../../data/annotation/html/SNPlocs.Hsapiens.dbSNP149.GRCh38.html">SNPlocs.Hsapiens.dbSNP149.GRCh38</a>, <a href="../../data/annotation/html/SNPlocs.Hsapiens.dbSNP150.GRCh38.html">SNPlocs.Hsapiens.dbSNP150.GRCh38</a>, <a href="../../data/annotation/html/SNPlocs.Hsapiens.dbSNP155.GRCh37.html">SNPlocs.Hsapiens.dbSNP155.GRCh37</a>, <a href="../../data/annotation/html/SNPlocs.Hsapiens.dbSNP155.GRCh38.html">SNPlocs.Hsapiens.dbSNP155.GRCh38</a>, <a href="../../data/annotation/html/XtraSNPlocs.Hsapiens.dbSNP144.GRCh37.html">XtraSNPlocs.Hsapiens.dbSNP144.GRCh37</a>, <a href="../../data/annotation/html/XtraSNPlocs.Hsapiens.dbSNP144.GRCh38.html">XtraSNPlocs.Hsapiens.dbSNP144.GRCh38</a>, <a href="../../data/experiment/html/BioPlex.html">BioPlex</a>, <a href="../../data/experiment/html/chipenrich.data.html">chipenrich.data</a>, <a href="../../data/experiment/html/GenomicDistributionsData.html">GenomicDistributionsData</a>, <a href="../../data/experiment/html/MethylSeqData.html">MethylSeqData</a>, <a href="../../data/experiment/html/sesameData.html">sesameData</a>, <a href="../../workflows/html/TCGAWorkflow.html">TCGAWorkflow</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/crispRdesignR/index.html">crispRdesignR</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/driveR/index.html">driveR</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/GRIN2/index.html">GRIN2</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/ICAMS/index.html">ICAMS</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/locuszoomr/index.html">locuszoomr</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/MAAPER/index.html">MAAPER</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/Mega2R/index.html">Mega2R</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/MicroSEC/index.html">MicroSEC</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/MOCHA/index.html">MOCHA</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/SeedMatchR/index.html">SeedMatchR</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/Signac/index.html">Signac</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/simMP/index.html">simMP</a></td> </tr> <tr> <td>Suggests Me</td> <td><a href="../../bioc/html/AlphaMissenseR.html">AlphaMissenseR</a>, <a href="../../bioc/html/AnnotationForge.html">AnnotationForge</a>, <a href="../../bioc/html/AnnotationHub.html">AnnotationHub</a>, <a href="../../bioc/html/DFplyr.html">DFplyr</a>, <a href="../../bioc/html/DiffBind.html">DiffBind</a>, <a href="../../bioc/html/epialleleR.html">epialleleR</a>, <a href="../../bioc/html/ExperimentHubData.html">ExperimentHubData</a>, <a href="../../bioc/html/fishpond.html">fishpond</a>, <a href="../../bioc/html/ldblock.html">ldblock</a>, <a href="../../bioc/html/megadepth.html">megadepth</a>, <a href="../../bioc/html/methrix.html">methrix</a>, <a href="../../bioc/html/OUTRIDER.html">OUTRIDER</a>, <a href="../../bioc/html/parglms.html">parglms</a>, <a href="../../bioc/html/QDNAseq.html">QDNAseq</a>, <a href="../../bioc/html/RAIDS.html">RAIDS</a>, <a href="../../bioc/html/regioneReloaded.html">regioneReloaded</a>, <a href="../../bioc/html/scTreeViz.html">scTreeViz</a>, <a href="../../bioc/html/splatter.html">splatter</a>, <a href="../../bioc/html/systemPipeR.html">systemPipeR</a>, <a href="../../bioc/html/TFutils.html">TFutils</a>, <a href="../../bioc/html/UCSC.utils.html">UCSC.utils</a>, <a href="../../data/annotation/html/BioMartGOGeneSets.html">BioMartGOGeneSets</a>, <a href="../../data/experiment/html/xcoredata.html">xcoredata</a>, <a href="../../workflows/html/seqpac.html">seqpac</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/gkmSVM/index.html">gkmSVM</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/polyRAD/index.html">polyRAD</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/Seurat/index.html">Seurat</a></td> </tr> <tr> <td>Links To Me</td> <td></td> </tr> <tr> <td>Build Report</td> <td><a href="https://bioconductor.org/checkResults/3.20/bioc-LATEST/GenomeInfoDb/">Build Report</a></td> </tr> </table> </details> <h3 id="archives">Package Archives</h3> <p>Follow <a href="/install/#install-bioconductor-packages">Installation</a> instructions to use this package in your R session.</p> <table class="full-width"> <tr> <td>Source Package</td> <td class="rpack"> <a onClick="javascript: pageTracker._trackPageview('../src/contrib/GenomeInfoDb_1.42.0.tar.gz'); " href="../src/contrib/GenomeInfoDb_1.42.0.tar.gz">GenomeInfoDb_1.42.0.tar.gz</a> </td> </tr> <tr> <td>Windows Binary (x86_64)</td> <td class="rpack"> <a onClick="javascript: pageTracker._trackPageview('../bin/windows/contrib/4.4/GenomeInfoDb_1.42.0.zip'); " href="../bin/windows/contrib/4.4/GenomeInfoDb_1.42.0.zip"> GenomeInfoDb_1.42.0.zip</a> (64-bit only) </td> </tr> <tr> <td>macOS Binary (x86_64)</td> <td class="rpack"> <a onClick="javascript: pageTracker._trackPageview('../bin/macosx/big-sur-x86_64/contrib/4.4/GenomeInfoDb_1.42.0.tgz'); " href="../bin/macosx/big-sur-x86_64/contrib/4.4/GenomeInfoDb_1.42.0.tgz">GenomeInfoDb_1.42.0.tgz</a> </td> </tr> <tr> <td>macOS Binary (arm64)</td> <td class="rpack"> <a onClick="javascript: pageTracker._trackPageview('../bin/macosx/big-sur-arm64/contrib/4.4/GenomeInfoDb_1.42.0.tgz'); " href="../bin/macosx/big-sur-arm64/contrib/4.4/GenomeInfoDb_1.42.0.tgz">GenomeInfoDb_1.42.0.tgz</a> </td> </tr> <tr> <td id="svn-source">Source Repository</td> <td>git clone https://git.bioconductor.org/packages/GenomeInfoDb</td> </tr> <tr> <td id="svn-source">Source Repository (Developer Access)</td> <td>git clone git@git.bioconductor.org:packages/GenomeInfoDb</td> </tr> <tr> <td>Bioc Package Browser</td> <td><a href="https://code.bioconductor.org/browse/GenomeInfoDb/RELEASE_3_20/">https://code.bioconductor.org/browse/GenomeInfoDb/</a></td> </tr> <tr> <td>Package Short Url</td> <td><a title="For citation in publications, etc., please use DOI: 10.18129/B9.bioc.GenomeInfoDb" href="/packages/GenomeInfoDb/">https://bioconductor.org/packages/GenomeInfoDb/</a></td> </tr> <tr> <td>Package Downloads Report</td> <td><a href="http://bioconductor.org/packages/stats/bioc/GenomeInfoDb/">Download Stats</a></td> </tr> </table> </div> </section> </div> </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 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