-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.html
3 lines (3 loc) · 15 KB
/
index.html
1
2
3
<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · RABBIT</title><meta name="title" content="Home · RABBIT"/><meta property="og:title" content="Home · RABBIT"/><meta property="twitter:title" content="Home · RABBIT"/><meta name="description" content="Documentation for RABBIT."/><meta property="og:description" content="Documentation for RABBIT."/><meta property="twitter:description" content="Documentation for RABBIT."/><script data-outdated-warner src="assets/warner.js"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/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/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="search_index.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/catppuccin-mocha.css" data-theme-name="catppuccin-mocha"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-macchiato.css" data-theme-name="catppuccin-macchiato"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-frappe.css" data-theme-name="catppuccin-frappe"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-latte.css" data-theme-name="catppuccin-latte"/><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>RABBIT</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a></li><li><input class="collapse-toggle" id="menuitem-2" type="checkbox"/><label class="tocitem" for="menuitem-2"><span class="docs-label">Guide</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="run_rabbit/">Run RABBIT</a></li><li><input class="collapse-toggle" id="menuitem-2-2" type="checkbox"/><label class="tocitem" for="menuitem-2-2"><span class="docs-label">Prepare Inputs</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="prepare_input/prepare_genofile/">Prepare genofile</a></li><li><a class="tocitem" href="prepare_input/prepare_pedinfo_designcode/">Prepare pedinfo: designcode</a></li><li><a class="tocitem" href="prepare_input/prepare_pedinfo_pedfile/">Prepare pedinfo: pedfile</a></li><li><a class="tocitem" href="prepare_input/prepare_phenofile/">Prepare phenofile</a></li><li><a class="tocitem" href="prepare_input/prepare_convert/">Prepare by converting </a></li></ul></li><li><a class="tocitem" href="understand_output/">Understand outputs</a></li><li><a class="tocitem" href="key_options/">Key options</a></li><li><a class="tocitem" href="statistical_framework/">Statistical framework</a></li></ul></li><li><input class="collapse-toggle" id="menuitem-3" type="checkbox"/><label class="tocitem" for="menuitem-3"><span class="docs-label">Pipeline</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="pipeline/s0_pipeline_overview/">Overview</a></li><li><a class="tocitem" href="pipeline/s1_magicsimulate/">S1 MagicSimulate</a></li><li><a class="tocitem" href="pipeline/s2_magicfilter/">S2 MagicFilter</a></li><li><a class="tocitem" href="pipeline/s3_magiccall/">S3 MagicCall</a></li><li><a class="tocitem" href="pipeline/s4_magicmap/">S4 MagicMap</a></li><li><a class="tocitem" href="pipeline/s5_magicimpute/">S5 MagicImpute</a></li><li><a class="tocitem" href="pipeline/s6_magicreconstruct/">S6 MagicReconstruct</a></li><li><a class="tocitem" href="pipeline/s7_magicscan/">S7 MagicScan</a></li></ul></li><li><a class="tocitem" href="rabbit_cli/">CLI</a></li><li><a class="tocitem" href="rabbit_api/">API</a></li><li><a class="tocitem" href="ref/">Citations</a></li></ul><div class="docs-version-selector field has-addons visible"><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"><option value="#" selected="selected">v1.0.0</option></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><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-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="RABBIT"><a class="docs-heading-anchor" href="#RABBIT">RABBIT</a><a id="RABBIT-1"></a><a class="docs-heading-anchor-permalink" href="#RABBIT" title="Permalink"></a></h1><p><strong>A statistical pipeline for genetic analysis in connected multiparental populations</strong></p><h3 id="Features"><a class="docs-heading-anchor" href="#Features">Features</a><a id="Features-1"></a><a class="docs-heading-anchor-permalink" href="#Features" title="Permalink"></a></h3><ul><li>Functions include data filtering, map construction, genotype imputation, and haplotype reconstruction.</li><li>Apply to many multiparental populations with shared inbred (or outbred) parents </li><li>Account for various sequencing errors such as allelic balance bias</li><li>Efficient for genomic data with hundreds of thousands of markers</li></ul><h3 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></h3><ol><li>Download and install Julia available at <a href="https://julialang.org/">https://julialang.org/</a></li><li>Download RABBIT repository</li><li>In a command shell, run</li></ol><pre><code class="nohighlight hljs">path/to/bin/julia.exe path/to/RABBIT/install_RABBIT.jl</code></pre><p>Alteratively, from the Julia (>= v1.9.7, 64-bit) REPL, run</p><pre><code class="language-julia hljs">include("path/to/RABBIT/install_RABBIT.jl")</code></pre><p>Similarly, use uninstall_RABBIT.jl for uninstalling RABBIT, up_RABBIT.jl for updating RABBIT, version_RABBIT.jl for printing the version number of each package in RABBIT, and test_RABBIT.jl for testing RABBIT (running the full test might take around one hour).</p><h3 id="Packages"><a class="docs-heading-anchor" href="#Packages">Packages</a><a id="Packages-1"></a><a class="docs-heading-anchor-permalink" href="#Packages" title="Permalink"></a></h3><p>Here is a list of key packages in RABBIT: <code>MagicBase</code> provides functions for visualizing or summarizing results, and each of <code>MagicSimulate</code>, <code>MagicFilter</code>, <code>MagicCall</code>, <code>MagicMap</code>, <code>MagicImpute</code>, <code>MagicReconstruct</code>, and <code>MagicScan</code> performs a single data analysis with function name being the lowercase of the package name. </p><table><tr><th style="text-align: left">Package name</th><th style="text-align: left">Description</th></tr><tr><td style="text-align: left"><code>MagicBase</code></td><td style="text-align: left">Basic data structures and functions</td></tr><tr><td style="text-align: left"><code>MagicSimulate</code></td><td style="text-align: left">Simulation of genotypic/phenotypic data</td></tr><tr><td style="text-align: left"><code>MagicFilter</code></td><td style="text-align: left">Filter genotypic data</td></tr><tr><td style="text-align: left"><code>MagicCall</code></td><td style="text-align: left">Single marker genotype calling</td></tr><tr><td style="text-align: left"><code>MagicMap</code></td><td style="text-align: left">Linkage map construction</td></tr><tr><td style="text-align: left"><code>MagicImpute</code></td><td style="text-align: left">Genotype imputation</td></tr><tr><td style="text-align: left"><code>MagicReconstruct</code></td><td style="text-align: left">Haplotype reconstruction</td></tr><tr><td style="text-align: left"><code>MagicScan</code></td><td style="text-align: left">Genome-wide QTL scan [EXPRIMENT]</td></tr></table><p><code>HMM</code>, <code>Pedigrees</code>, <code>MagicPrior</code>, <code>MagicLD</code>, <code>MagicLinkage</code> and <code>SpectralEmbedding</code> are supporting packages. <code>RABBITCLI</code> includes RABBIT's Command Line Interface (CLI). <code>RABBITDocs</code> is only for automatically generating documents. All packages are installed in order by running <code>install_RABBIT.jl</code> as described above.</p><h3 id="Versions"><a class="docs-heading-anchor" href="#Versions">Versions</a><a id="Versions-1"></a><a class="docs-heading-anchor-permalink" href="#Versions" title="Permalink"></a></h3><p>The RABBITCLI version is the same as that of RABBIT. To check the versions of the RABBIT packages, run</p><pre><code class="language-julia hljs">using RABBITCLI
rabbitversion()</code></pre><div><div style = "float: left;"><span>15×2 DataFrame</span></div><div style = "clear: both;"></div></div><div class = "data-frame" style = "overflow-x: scroll;"><table class = "data-frame" style = "margin-bottom: 6px;"><thead><tr class = "header"><th class = "rowNumber" style = "font-weight: bold; text-align: right;">Row</th><th style = "text-align: left;">pkgname</th><th style = "text-align: left;">version</th></tr><tr class = "subheader headerLastRow"><th class = "rowNumber" style = "font-weight: bold; text-align: right;"></th><th title = "String" style = "text-align: left;">String</th><th title = "VersionNumber" style = "text-align: left;">VersionN…</th></tr></thead><tbody><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">1</td><td style = "text-align: left;">HMM</td><td style = "text-align: left;">1.0.0</td></tr><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">2</td><td style = "text-align: left;">Pedigrees</td><td style = "text-align: left;">1.0.0</td></tr><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">3</td><td style = "text-align: left;">MagicPrior</td><td style = "text-align: left;">1.0.0</td></tr><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">4</td><td style = "text-align: left;">MagicBase</td><td style = "text-align: left;">1.0.0</td></tr><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">5</td><td style = "text-align: left;">MagicSimulate</td><td style = "text-align: left;">1.0.0</td></tr><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">6</td><td style = "text-align: left;">MagicReconstruct</td><td style = "text-align: left;">1.0.0</td></tr><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">7</td><td style = "text-align: left;">MagicCall</td><td style = "text-align: left;">1.0.0</td></tr><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">8</td><td style = "text-align: left;">MagicFilter</td><td style = "text-align: left;">1.0.0</td></tr><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">9</td><td style = "text-align: left;">MagicImpute</td><td style = "text-align: left;">1.0.0</td></tr><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">10</td><td style = "text-align: left;">SpectralEmbedding</td><td style = "text-align: left;">1.0.0</td></tr><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">11</td><td style = "text-align: left;">MagicLD</td><td style = "text-align: left;">1.0.0</td></tr><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">12</td><td style = "text-align: left;">MagicLinkage</td><td style = "text-align: left;">1.0.0</td></tr><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">13</td><td style = "text-align: left;">MagicMap</td><td style = "text-align: left;">1.0.0</td></tr><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">14</td><td style = "text-align: left;">MagicScan</td><td style = "text-align: left;">1.0.0</td></tr><tr><td class = "rowNumber" style = "font-weight: bold; text-align: right;">15</td><td style = "text-align: left;">RABBITCLI</td><td style = "text-align: left;">1.0.0</td></tr></tbody></table></div></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="run_rabbit/">Run RABBIT »</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="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Friday 17 January 2025 15:55">Friday 17 January 2025</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>