Bioconductor - scDataviz

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for the devel version, see <a href="/packages/devel/bioc/html/scDataviz.html">scDataviz</a>.</p> <h2>scDataviz: single cell dataviz and downstream analyses</h2> <div class="sidebar-box" id="badges-box"> <section class="badges"> <a href="#archives"> <img src="/shields/availability/release/scDataviz.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/scDataviz/"> <img src="/shields/downloads/release/scDataviz.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/scdataviz"> <img src="/shields/posts/scDataviz.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/scDataviz.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/scDataviz/"> <img src="/shields/build/release/bioc/scDataviz.svg" alt="Build results badge" title="build results; click for full report" /> </a> <a href="https://bioconductor.org/checkResults/release/bioc-LATEST/scDataviz/"> <img src="/shields/lastcommit/release/bioc/scDataviz.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/scDataviz.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.scDataviz" > 10.18129/B9.bioc.scDataviz </a> </p> </div> <p><br></p> <div class="package-info"> <p> <strong>Bioconductor version:</strong> Release (3.20) </p> <p> In the single cell World, which includes flow cytometry, mass cytometry, single-cell RNA-seq (scRNA-seq), and others, there is a need to improve data visualisation and to bring analysis capabilities to researchers even from non-technical backgrounds. scDataviz attempts to fit into this space, while also catering for advanced users. Additonally, due to the way that scDataviz is designed, which is based on SingleCellExperiment, it has a 'plug and play' feel, and immediately lends itself as flexibile and compatibile with studies that go beyond scDataviz. Finally, the graphics in scDataviz are generated via the ggplot engine, which means that users can 'add on' features to these with ease. </p> <p> <strong>Author:</strong> Kevin Blighe [aut, cre] <p /> <p> <strong>Maintainer:</strong> Kevin Blighe <kevin at clinicalbioinformatics.co.uk> </p> <div id="bioc-citation-outer"> <strong>Citation (from within R, enter <code>citation("scDataviz")</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("scDataviz") </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("scDataviz")</code></pre> <table> <tr> <td>scDataviz: single cell dataviz and downstream analyses</td> <td> <a href="../vignettes/scDataviz/inst/doc/scDataviz.html">HTML</a> </td> <td> <a onClick="javascript: pageTracker._trackPageview('../vignettes/scDataviz/inst/doc/scDataviz.R'); " href="../vignettes/scDataviz/inst/doc/scDataviz.R">R Script</a> </td> </tr> <tr> <td>Reference Manual</td> <td> <a onClick="javascript: pageTracker._trackPageview('../manuals/scDataviz/man/scDataviz.pdf'); " href="../manuals/scDataviz/man/scDataviz.pdf">PDF</a> </td> </tr> <tr> <td>NEWS</td> <td> <a href="../news/scDataviz/NEWS">Text</a> </td> </tr> </table> <p> <div class="info-section-button-padding"> <a class="brand-border-button" href="https://support.bioconductor.org/tag/scdataviz"> <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#___DataImport">DataImport</a>, <a href="../../BiocViews.html#___FlowCytometry">FlowCytometry</a>, <a href="../../BiocViews.html#___GeneExpression">GeneExpression</a>, <a href="../../BiocViews.html#___ImmunoOncology">ImmunoOncology</a>, <a href="../../BiocViews.html#___MassSpectrometry">MassSpectrometry</a>, <a href="../../BiocViews.html#___RNASeq">RNASeq</a>, <a href="../../BiocViews.html#___SingleCell">SingleCell</a>, <a href="../../BiocViews.html#___Software">Software</a>, <a href="../../BiocViews.html#___Transcription">Transcription</a></td> </tr> <tr> <td>Version</td> <td>1.16.0</td> </tr> <tr id="since"> <td>In Bioconductor since</td> <td>BioC 3.12 (R-4.0) (4 years)</td> </tr> <tr> <td>License</td> <td>GPL-3</td> </tr> <tr> <td>Depends</td> <td>R (>= 4.0), <a href="../../bioc/html/S4Vectors.html">S4Vectors</a>, <a href="../../bioc/html/SingleCellExperiment.html">SingleCellExperiment</a></td> </tr> <tr> <td>Imports</td> <td><a class="cran_package" href="http://cran.rstudio.com/web/packages/ggplot2/index.html">ggplot2</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/ggrepel/index.html">ggrepel</a>, <a href="../../bioc/html/flowCore.html">flowCore</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/umap/index.html">umap</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/Seurat/index.html">Seurat</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/reshape2/index.html">reshape2</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/scales/index.html">scales</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/RColorBrewer/index.html">RColorBrewer</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/corrplot/index.html">corrplot</a>, stats, grDevices, graphics, utils, <a class="cran_package" href="http://cran.rstudio.com/web/packages/MASS/index.html">MASS</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/matrixStats/index.html">matrixStats</a>, methods</td> </tr> <tr> <td>System Requirements</td> <td></td> </tr> <tr> <td>URL</td> <td><a href="https://github.com/kevinblighe/scDataviz">https://github.com/kevinblighe/scDataviz</a> </td> </tr> <tr> <td>Bug Reports</td> <td><a href="https://github.com/kevinblighe/scDataviz/issues">https://github.com/kevinblighe/scDataviz/issues</a> </td> </tr> </table> <details> <summary class="package-details">See More</summary> <table class="full-width"> <tr> <td>Suggests</td> <td><a href="../../bioc/html/PCAtools.html">PCAtools</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/cowplot/index.html">cowplot</a>, <a href="../../bioc/html/BiocGenerics.html">BiocGenerics</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/RUnit/index.html">RUnit</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/knitr/index.html">knitr</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/kableExtra/index.html">kableExtra</a>, <a class="cran_package" href="http://cran.rstudio.com/web/packages/rmarkdown/index.html">rmarkdown</a></td> </tr> <tr> <td>Linking To</td> <td></td> </tr> <tr> <td>Enhances</td> <td></td> </tr> <tr> <td>Depends On Me</td> <td></td> </tr> <tr> <td>Imports Me</td> <td></td> </tr> <tr> <td>Suggests Me</td> <td></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/scDataviz/">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/scDataviz_1.16.0.tar.gz'); " href="../src/contrib/scDataviz_1.16.0.tar.gz">scDataviz_1.16.0.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/scDataviz_1.16.0.zip'); " href="../bin/windows/contrib/4.4/scDataviz_1.16.0.zip"> scDataviz_1.16.0.zip</a> </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/scDataviz_1.16.0.tgz'); " href="../bin/macosx/big-sur-x86_64/contrib/4.4/scDataviz_1.16.0.tgz">scDataviz_1.16.0.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/scDataviz_1.16.0.tgz'); " href="../bin/macosx/big-sur-arm64/contrib/4.4/scDataviz_1.16.0.tgz">scDataviz_1.16.0.tgz</a> </td> </tr> <tr> <td id="svn-source">Source Repository</td> <td>git clone https://git.bioconductor.org/packages/scDataviz</td> </tr> <tr> <td id="svn-source">Source Repository (Developer Access)</td> <td>git clone git@git.bioconductor.org:packages/scDataviz</td> </tr> <tr> <td>Bioc Package Browser</td> <td><a href="https://code.bioconductor.org/browse/scDataviz/RELEASE_3_20/">https://code.bioconductor.org/browse/scDataviz/</a></td> </tr> <tr> <td>Package Short Url</td> <td><a title="For citation in publications, etc., please use DOI: 10.18129/B9.bioc.scDataviz" href="/packages/scDataviz/">https://bioconductor.org/packages/scDataviz/</a></td> </tr> <tr> <td>Package Downloads Report</td> <td><a href="http://bioconductor.org/packages/stats/bioc/scDataviz/">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 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 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Bioconductor - scDataviz