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 <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · Microbiome.jl</title><script data-outdated-warner src="assets/warner.js"></script><link rel="canonical" href="http://docs.ecojulia.org/BiobakeryUtils.jl/stable/"/><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"><div class="docs-package-name"><span class="docs-autofit"><a href>Microbiome.jl</a></span></div><form class="docs-search" action="search/"><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>Home</a><ul class="internal"><li><a class="tocitem" href="#Description"><span>Description</span></a></li><li><a class="tocitem" href="#Installation"><span>Installation</span></a></li></ul></li><li><a class="tocitem" href="samples_features/">Samples and features</a></li><li><a class="tocitem" href="profiles/">Profiles and Communities</a></li><li><a class="tocitem" href="diversity/">Diversity measures</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>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/EcoJulia/Microbiome.jl/blob/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="Microbiome.jl"><a class="docs-heading-anchor" href="#Microbiome.jl">Microbiome.jl</a><a id="Microbiome.jl-1"></a><a class="docs-heading-anchor-permalink" href="#Microbiome.jl" title="Permalink"></a></h1><h2 id="Description"><a class="docs-heading-anchor" href="#Description">Description</a><a id="Description-1"></a><a class="docs-heading-anchor-permalink" href="#Description" title="Permalink"></a></h2><p>Microbiome.jl is a package for manipulating and analyzing microbiome and microbial community data.</p><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>Install Microbiome from the Julia REPL:</p><pre><code class="language-julia hljs">julia&gt; using Pkg
 
-julia&gt; pkg&quot;add Microbiome&quot;</code></pre><p>If you are interested in the cutting edge of the development, please check out the master branch to try new features before release.</p><pre><code class="language-julia hljs">julia&gt; pkg&quot;add Microbiome#master&quot;</code></pre><ul><li><a href="samples_features/#Samples-and-Features">Samples and Features</a></li><li class="no-marker"><ul><li><a href="samples_features/#Sample-types">Sample types</a></li><li><a href="samples_features/#Feature-Types">Feature Types</a></li><li><a href="samples_features/#Types-and-Methods">Types and Methods</a></li></ul></li><li><a href="profiles/#Working-with-microbial-abundances">Working with microbial abundances</a></li><li class="no-marker"><ul><li><a href="profiles/#Accessing-CommunityProfile-contents">Accessing <code>CommunityProfile</code> contents</a></li><li><a href="profiles/#Indexing-and-selecting">Indexing and selecting</a></li><li><a href="profiles/#working-metadata">Working with metadata</a></li><li><a href="profiles/#Importing-from-tabular-data">Importing from tabular data</a></li><li><a href="profiles/#Types-and-Methods">Types and Methods</a></li></ul></li><li><a href="diversity/#Diversity-measures-on-communities-and-samples">Diversity measures on communities and samples</a></li><li class="no-marker"><ul><li><a href="diversity/#Alpha-Diversity">Alpha Diversity</a></li><li><a href="diversity/#Beta-Diversity">Beta Diversity</a></li></ul></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="samples_features/">Samples and features »</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 0.27.24 on <span class="colophon-date" title="Thursday 23 March 2023 15:49">Thursday 23 March 2023</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+julia&gt; pkg&quot;add Microbiome&quot;</code></pre><p>If you are interested in the cutting edge of the development, please check out the master branch to try new features before release.</p><pre><code class="language-julia hljs">julia&gt; pkg&quot;add Microbiome#master&quot;</code></pre><ul><li><a href="samples_features/#Samples-and-Features">Samples and Features</a></li><li class="no-marker"><ul><li><a href="samples_features/#Sample-types">Sample types</a></li><li><a href="samples_features/#Feature-Types">Feature Types</a></li><li><a href="samples_features/#Types-and-Methods">Types and Methods</a></li></ul></li><li><a href="profiles/#Working-with-microbial-abundances">Working with microbial abundances</a></li><li class="no-marker"><ul><li><a href="profiles/#Accessing-CommunityProfile-contents">Accessing <code>CommunityProfile</code> contents</a></li><li><a href="profiles/#Indexing-and-selecting">Indexing and selecting</a></li><li><a href="profiles/#working-metadata">Working with metadata</a></li><li><a href="profiles/#Importing-from-tabular-data">Importing from tabular data</a></li><li><a href="profiles/#Types-and-Methods">Types and Methods</a></li></ul></li><li><a href="diversity/#Diversity-measures-on-communities-and-samples">Diversity measures on communities and samples</a></li><li class="no-marker"><ul><li><a href="diversity/#Alpha-Diversity">Alpha Diversity</a></li><li><a href="diversity/#Beta-Diversity">Beta Diversity</a></li></ul></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="samples_features/">Samples and features »</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="Friday 18 August 2023 18:29">Friday 18 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>