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Additional information for Guyomar et al 2018, accepted in Microbiome
cguyomar/aphid_microbiome_website
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<!DOCTYPE html> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta charset="utf-8" /> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <meta name="generator" content="pandoc" /> <title></title> <script src="site_libs/jquery-1.11.3/jquery.min.js"></script> <meta name="viewport" content="width=device-width, initial-scale=1" /> <link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script> <script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script> <script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script> <script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script> <link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" /> <script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script> <script src="site_libs/navigation-1.1/tabsets.js"></script> <style type="text/css"> h1 { font-size: 34px; } h1.title { font-size: 38px; } h2 { font-size: 30px; } h3 { font-size: 24px; } h4 { font-size: 18px; } h5 { font-size: 16px; } h6 { font-size: 12px; } .table th:not([align]) { text-align: left; } </style> </head> <body> <style type = "text/css"> .main-container { max-width: 940px; margin-left: auto; margin-right: auto; } code { color: inherit; background-color: rgba(0, 0, 0, 0.04); } img { max-width:100%; height: auto; } .tabbed-pane { padding-top: 12px; } button.code-folding-btn:focus { outline: none; } </style> <style type="text/css"> /* padding for bootstrap navbar */ body { padding-top: 51px; padding-bottom: 40px; } /* offset scroll position for anchor links (for fixed navbar) */ .section h1 { padding-top: 56px; margin-top: -56px; } .section h2 { padding-top: 56px; margin-top: -56px; } .section h3 { padding-top: 56px; margin-top: -56px; } .section h4 { padding-top: 56px; margin-top: -56px; } .section h5 { padding-top: 56px; margin-top: -56px; } .section h6 { padding-top: 56px; margin-top: -56px; } </style> <script> // manage active state of menu based on current page $(document).ready(function () { // active menu anchor href = window.location.pathname href = href.substr(href.lastIndexOf('/') + 1) if (href === "") href = "index.html"; var menuAnchor = $('a[href="' + href + '"]'); // mark it active menuAnchor.parent().addClass('active'); // if it's got a parent navbar menu mark it active as well menuAnchor.closest('li.dropdown').addClass('active'); }); </script> <div class="container-fluid main-container"> <!-- tabsets --> <script> $(document).ready(function () { window.buildTabsets("TOC"); }); </script> <!-- code folding --> <script> $(document).ready(function () { // move toc-ignore selectors from section div to header $('div.section.toc-ignore') .removeClass('toc-ignore') .children('h1,h2,h3,h4,h5').addClass('toc-ignore'); // establish options var options = { selectors: "h1,h2,h3", theme: "bootstrap3", context: '.toc-content', hashGenerator: function (text) { return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase(); }, ignoreSelector: ".toc-ignore", scrollTo: 0 }; options.showAndHide = true; options.smoothScroll = true; // tocify var toc = $("#TOC").tocify(options).data("toc-tocify"); }); </script> <style type="text/css"> #TOC { margin: 25px 0px 20px 0px; } @media (max-width: 768px) { #TOC { position: relative; width: 100%; } } .toc-content { padding-left: 30px; padding-right: 40px; } div.main-container { max-width: 1200px; } div.tocify { width: 20%; max-width: 260px; max-height: 85%; } @media (min-width: 768px) and (max-width: 991px) { div.tocify { width: 25%; } } @media (max-width: 767px) { div.tocify { width: 100%; max-width: none; } } .tocify ul, .tocify li { line-height: 20px; } .tocify-subheader .tocify-item { font-size: 0.90em; padding-left: 25px; text-indent: 0; } .tocify .list-group-item { border-radius: 0px; } </style> <!-- setup 3col/9col grid for toc_float and main content --> <div class="row-fluid"> <div class="col-xs-12 col-sm-4 col-md-3"> <div id="TOC" class="tocify"> </div> </div> <div class="toc-content col-xs-12 col-sm-8 col-md-9"> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <a class="navbar-brand" href="index.html"></a> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> <a href="index.html">Home</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> Mapping on reference genome set <span class="caret"></span> </a> <ul class="dropdown-menu" role="menu"> <li> <a href="mapping.html">Scripts</a> </li> <li> <a href="mapping_results.html">Mapping table</a> </li> </ul> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> Unmapped analysis <span class="caret"></span> </a> <ul class="dropdown-menu" role="menu"> <li> <a href="unmapped.html">Scripts</a> </li> <li> <a href="by_sample-report.html">Centrifuge results by sample</a> </li> <li> <a href="all-report.html">Centrifuge results pooled</a> </li> </ul> </li> <li> <a href="phylogeny.html">Phylogenetic analysis</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> <div class="fluid-row" id="header"> </div> <div id="aphid_microbiome_website" class="section level1"> <h1>Aphid_microbiome_website</h1> </div> </div> </div> </div> <script> // add bootstrap table styles to pandoc tables function bootstrapStylePandocTables() { $('tr.header').parent('thead').parent('table').addClass('table table-condensed'); } $(document).ready(function () { bootstrapStylePandocTables(); }); </script> <!-- dynamically load mathjax for compatibility with self-contained --> <script> (function () { var script = document.createElement("script"); script.type = "text/javascript"; script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"; document.getElementsByTagName("head")[0].appendChild(script); })(); </script> </body> </html>
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