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 <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Getting started · scVI</title><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="index.html"><img src="assets/logo.svg" alt="scVI logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="index.html">scVI</a></span></div><form class="docs-search" action="search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li class="is-active"><a class="tocitem" href="index.html">Getting started</a><ul class="internal"><li><a class="tocitem" href="#Overview"><span>Overview</span></a></li><li><a class="tocitem" href="#Installation"><span>Installation</span></a></li><li><a class="tocitem" href="#Contents"><span>Contents</span></a></li></ul></li><li><a class="tocitem" href="DataProcessing.html">Data processing</a></li><li><a class="tocitem" href="scVAE.html">The scVAE model</a></li><li><a class="tocitem" href="scLDVAE.html">The scLDVAE model</a></li><li><a class="tocitem" href="Training.html">Model training</a></li><li><a class="tocitem" href="Evaluation.html">Model evaluation</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="index.html">Getting started</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="index.html">Getting started</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/maren-ha/scVI.jl/blob/origin/main/docs/src/index.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="scVI.jl"><a class="docs-heading-anchor" href="#scVI.jl">scVI.jl</a><a id="scVI.jl-1"></a><a class="docs-heading-anchor-permalink" href="#scVI.jl" title="Permalink"></a></h1><p><img src="assets/scvi-julia-logo.jpg" alt/></p><p>A Julia package for fitting VAEs to single-cell data using count distributions.  Based on the Python implementation in the <a href="https://github.com/scverse/scvi-tools"><code>scvi-tools</code></a> package. </p><h2 id="Overview"><a class="docs-heading-anchor" href="#Overview">Overview</a><a id="Overview-1"></a><a class="docs-heading-anchor-permalink" href="#Overview" title="Permalink"></a></h2><p>The scVI model was first proposed in <a href="https://doi.org/10.1038/s41592-018-0229-2">Lopez R, Regier J, Cole MB <em>et al.</em> Deep generative modeling for single-cell transcriptomics. <em>Nat Methods</em> <strong>15</strong>, 1053-1058 (2018)</a>. </p><p>More on the much more extensive Python package ecosystem <a href="https://github.com/scverse/scvi-tools"><code>scvi-tools</code></a> can be found on the  <a href="https://scvi-tools.org">website</a> and in the corresponding paper <a href="https://doi.org/10.1038/s41587-021-01206-w">Gayoso A, Lopez R, Xing G. <em>et al.</em> A Python library for probabilistic analysis of single-cell omics data. <em>Nat Biotechnol</em> <strong>40</strong>, 163–166 (2022)</a>. </p><p>This is the documentation for the Julia version implementing basic functionality, including the following (non-exhausive list): </p><ul><li>standard and linearly decoded VAE models </li><li>support for negative binomial generative distribution with and without zero-inflation </li><li>different ways of specifying the dispersion parameter </li><li>store data in a (very basic) Julia version of the Python <a href="https://anndata.readthedocs.io/en/latest/"><code>AnnData</code></a> objects </li><li>several built-in datasets </li><li>training routines supporting a wide range of customisable hyperparameters </li></ul><h2 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h2><p>The package can be downloaded from the <a href="https://github.com/maren-ha/scVI.jl">Github repo</a> and added with the Julia package manager via </p><pre><code class="nohighlight hljs">julia&gt; ]
-pkg &gt; add &quot;https://github.com/maren-ha/scVI.jl&quot;</code></pre><p>or alternatively by </p><pre><code class="nohighlight hljs">julia&gt; using Pkg; Pkg.add(url=&quot;https://github.com/maren-ha/scVI.jl&quot;)</code></pre><h2 id="Contents"><a class="docs-heading-anchor" href="#Contents">Contents</a><a id="Contents-1"></a><a class="docs-heading-anchor-permalink" href="#Contents" title="Permalink"></a></h2><ul><li><a href="DataProcessing.html#Data-processing">Data processing</a></li><li class="no-marker"><ul><li><a href="DataProcessing.html#AnnData-object-ind-I/O"><code>AnnData</code> object ind I/O</a></li><li><a href="DataProcessing.html#Library-size-and-normalization">Library size and normalization</a></li><li><a href="DataProcessing.html#Filtering">Filtering</a></li><li><a href="DataProcessing.html#Simple-transformations">Simple transformations</a></li><li><a href="DataProcessing.html#Dimension-reduction">Dimension reduction</a></li><li><a href="DataProcessing.html#Highly-variable-genes">Highly variable genes</a></li><li><a href="DataProcessing.html#Loading-built-in-datasets">Loading built-in datasets</a></li></ul></li><li><a href="scVAE.html#The-scVAE-model">The scVAE model</a></li><li class="no-marker"><ul><li><a href="scVAE.html#Encoder">Encoder</a></li><li><a href="scVAE.html#Decoder">Decoder</a></li><li><a href="scVAE.html#VAE-model">VAE model</a></li></ul></li><li><a href="scLDVAE.html#The-scLDVAE-model">The scLDVAE model</a></li><li><a href="Training.html#Model-training">Model training</a></li><li><a href="Evaluation.html#Model-evaluation">Model evaluation</a></li><li class="no-marker"><ul><li><a href="Evaluation.html#Extract-latent-representations">Extract latent representations</a></li><li><a href="Evaluation.html#Dimension-reduction-and-plotting">Dimension reduction and plotting</a></li><li><a href="Evaluation.html#Sampling-from-the-trained-model">Sampling from the trained model</a></li></ul></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="DataProcessing.html">Data processing »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 14 August 2023 08:45">Monday 14 August 2023</span>. Using Julia version 1.7.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+pkg &gt; add &quot;https://github.com/maren-ha/scVI.jl&quot;</code></pre><p>or alternatively by </p><pre><code class="nohighlight hljs">julia&gt; using Pkg; Pkg.add(url=&quot;https://github.com/maren-ha/scVI.jl&quot;)</code></pre><h2 id="Contents"><a class="docs-heading-anchor" href="#Contents">Contents</a><a id="Contents-1"></a><a class="docs-heading-anchor-permalink" href="#Contents" title="Permalink"></a></h2><ul><li><a href="DataProcessing.html#Data-processing">Data processing</a></li><li class="no-marker"><ul><li><a href="DataProcessing.html#AnnData-object-ind-I/O"><code>AnnData</code> object ind I/O</a></li><li><a href="DataProcessing.html#Library-size-and-normalization">Library size and normalization</a></li><li><a href="DataProcessing.html#Filtering">Filtering</a></li><li><a href="DataProcessing.html#Simple-transformations">Simple transformations</a></li><li><a href="DataProcessing.html#Dimension-reduction">Dimension reduction</a></li><li><a href="DataProcessing.html#Highly-variable-genes">Highly variable genes</a></li><li><a href="DataProcessing.html#Plotting">Plotting</a></li><li><a href="DataProcessing.html#Loading-built-in-datasets">Loading built-in datasets</a></li></ul></li><li><a href="scVAE.html#The-scVAE-model">The scVAE model</a></li><li class="no-marker"><ul><li><a href="scVAE.html#Encoder">Encoder</a></li><li><a href="scVAE.html#Decoder">Decoder</a></li><li><a href="scVAE.html#VAE-model">VAE model</a></li></ul></li><li><a href="scLDVAE.html#The-scLDVAE-model">The scLDVAE model</a></li><li><a href="Training.html#Model-training">Model training</a></li><li><a href="Evaluation.html#Model-evaluation">Model evaluation</a></li><li class="no-marker"><ul><li><a href="Evaluation.html#Extract-latent-representations">Extract latent representations</a></li><li><a href="Evaluation.html#Dimension-reduction-and-plotting">Dimension reduction and plotting</a></li><li><a href="Evaluation.html#Sampling-from-the-trained-model">Sampling from the trained model</a></li></ul></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="DataProcessing.html">Data processing »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 14 August 2023 12:17">Monday 14 August 2023</span>. Using Julia version 1.7.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>