Skip to content

Commit

Permalink
Add files via upload
Browse files Browse the repository at this point in the history
  • Loading branch information
mfiorini9 authored Jun 14, 2024
1 parent 25c9118 commit ee7ab41
Show file tree
Hide file tree
Showing 48 changed files with 12,562 additions and 0 deletions.
148 changes: 148 additions & 0 deletions site/404.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,148 @@
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<link rel="shortcut icon" href="/img/favicon.ico" />
<title>Ensemblex</title>
<link rel="stylesheet" href="/css/theme.css" />
<link rel="stylesheet" href="/css/theme_extra.css" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/styles/github.min.css" />

<!--[if lt IE 9]>
<script src="/js/html5shiv.min.js"></script>
<![endif]-->
<script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/highlight.min.js"></script>
<script>hljs.highlightAll();</script>
</head>

<body class="wy-body-for-nav" role="document">

<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side stickynav">
<div class="wy-side-scroll">
<div class="wy-side-nav-search">
<a href="/." class="icon icon-home"> Ensemblex
</a><div role="search">
<form id ="rtd-search-form" class="wy-form" action="//search.html" method="get">
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" title="Type search term here" />
</form>
</div>
</div>

<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<ul>
<li class="toctree-l1"><a class="reference internal" href="/.">Home</a>
</li>
</ul>
<p class="caption"><span class="caption-text">The Ensemblex algorithm</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="/overview/">Ensemblex algorithm overview</a>
</li>
</ul>
<p class="caption"><span class="caption-text">The Ensemblex Pipeline</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="/overview_pipeline/">Ensemblex pipeline overview</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="/installation/">Installation</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="/Step0/">Step 1: Set up</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="/Step1/">Step 2: Preparation of input files</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="/Step2/">Step 3: Genetic demultiplexing by constituent tools</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="/Step3/">Step 4: Application of Ensemblex</a>
</li>
</ul>
<p class="caption"><span class="caption-text">Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="/reference/">Execution parameters</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="/outputs/">Ensemblex outputs</a>
</li>
</ul>
<p class="caption"><span class="caption-text">Tutorial</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="/midbrain_download/">Downloading data</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="/Dataset1/">Ensemblex with prior genotype information</a>
</li>
</ul>
<p class="caption"><span class="caption-text">About</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="/contributing/">Help and Feedback</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="/Acknowledgement/">Acknowledgement</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="/LICENSE/">License</a>
</li>
</ul>
</div>
</div>
</nav>

<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" role="navigation" aria-label="Mobile navigation menu">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="/.">Ensemblex</a>

</nav>
<div class="wy-nav-content">
<div class="rst-content"><div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="/." class="icon icon-home" aria-label="Docs"></a> &raquo;</li>
<li class="wy-breadcrumbs-aside">
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div class="section" itemprop="articleBody">


<h1 id="404-page-not-found">404</h1>

<p><strong>Page not found</strong></p>


</div>
</div><footer>

<hr/>

<div role="contentinfo">
<!-- Copyright etc -->
</div>

Built with <a href="https://www.mkdocs.org/">MkDocs</a> using a <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>

</div>
</div>

</section>

</div>

<div class="rst-versions" role="note" aria-label="Versions">
<span class="rst-current-version" data-toggle="rst-current-version">



</span>
</div>
<script src="/js/jquery-3.6.0.min.js"></script>
<script>var base_url = "/";</script>
<script src="/js/theme_extra.js"></script>
<script src="/js/theme.js"></script>
<script src="/search/main.js"></script>
<script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>

</body>
</html>
164 changes: 164 additions & 0 deletions site/Acknowledgement/index.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,164 @@
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><link rel="canonical" href="https://neurobioinfo.github.io/Acknowledgement/" />
<link rel="shortcut icon" href="../img/favicon.ico" />
<title>Acknowledgement - Ensemblex</title>
<link rel="stylesheet" href="../css/theme.css" />
<link rel="stylesheet" href="../css/theme_extra.css" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/styles/github.min.css" />

<script>
// Current page data
var mkdocs_page_name = "Acknowledgement";
var mkdocs_page_input_path = "Acknowledgement.md";
var mkdocs_page_url = "/Acknowledgement/";
</script>

<!--[if lt IE 9]>
<script src="../js/html5shiv.min.js"></script>
<![endif]-->
<script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/highlight.min.js"></script>
<script>hljs.highlightAll();</script>
</head>

<body class="wy-body-for-nav" role="document">

<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side stickynav">
<div class="wy-side-scroll">
<div class="wy-side-nav-search">
<a href=".." class="icon icon-home"> Ensemblex
</a><div role="search">
<form id ="rtd-search-form" class="wy-form" action="../search.html" method="get">
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" title="Type search term here" />
</form>
</div>
</div>

<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<ul>
<li class="toctree-l1"><a class="reference internal" href="..">Home</a>
</li>
</ul>
<p class="caption"><span class="caption-text">The Ensemblex algorithm</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../overview/">Ensemblex algorithm overview</a>
</li>
</ul>
<p class="caption"><span class="caption-text">The Ensemblex Pipeline</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../overview_pipeline/">Ensemblex pipeline overview</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="../installation/">Installation</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="../Step0/">Step 1: Set up</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="../Step1/">Step 2: Preparation of input files</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="../Step2/">Step 3: Genetic demultiplexing by constituent tools</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="../Step3/">Step 4: Application of Ensemblex</a>
</li>
</ul>
<p class="caption"><span class="caption-text">Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../reference/">Execution parameters</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="../outputs/">Ensemblex outputs</a>
</li>
</ul>
<p class="caption"><span class="caption-text">Tutorial</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../midbrain_download/">Downloading data</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="../Dataset1/">Ensemblex with prior genotype information</a>
</li>
</ul>
<p class="caption"><span class="caption-text">About</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="../contributing/">Help and Feedback</a>
</li>
<li class="toctree-l1 current"><a class="reference internal current" href="./">Acknowledgement</a>
<ul class="current">
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../LICENSE/">License</a>
</li>
</ul>
</div>
</div>
</nav>

<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" role="navigation" aria-label="Mobile navigation menu">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="..">Ensemblex</a>

</nav>
<div class="wy-nav-content">
<div class="rst-content"><div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href=".." class="icon icon-home" aria-label="Docs"></a> &raquo;</li>
<li>About &raquo;</li>
<li class="breadcrumb-item active">Acknowledgement</li>
<li class="wy-breadcrumbs-aside">
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div class="section" itemprop="articleBody">

<h2 id="acknowledgement">Acknowledgement</h2>
<p>The Ensemblex pipeline was produced for projects funded by the Canadian Institute of Health Research and Michael J. Fox Foundation Parkinson's Progression Markers Initiative (MJFF PPMI) in collaboration with The Neuro's Early Drug Discovery Unit (EDDU), McGill University. It is written by <a href="https://github.com/fiorini9">Michael Fiorini</a> and <a href="https://github.com/saeidamiri1">Saeid Amiri</a> with supervision from <a href="https://github.com/RhalenaThomas">Rhalena Thomas</a> and Sali Farhan at the Montreal Neurological Institute-Hospital. Copyright belongs <a href="https://github.com/neurobioinfo">MNI BIOINFO CORE</a>. </p>

</div>
</div><footer>
<div class="rst-footer-buttons" role="navigation" aria-label="Footer Navigation">
<a href="../contributing/" class="btn btn-neutral float-left" title="Help and Feedback"><span class="icon icon-circle-arrow-left"></span> Previous</a>
<a href="../LICENSE/" class="btn btn-neutral float-right" title="License">Next <span class="icon icon-circle-arrow-right"></span></a>
</div>

<hr/>

<div role="contentinfo">
<!-- Copyright etc -->
</div>

Built with <a href="https://www.mkdocs.org/">MkDocs</a> using a <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>

</div>
</div>

</section>

</div>

<div class="rst-versions" role="note" aria-label="Versions">
<span class="rst-current-version" data-toggle="rst-current-version">


<span><a href="../contributing/" style="color: #fcfcfc">&laquo; Previous</a></span>


<span><a href="../LICENSE/" style="color: #fcfcfc">Next &raquo;</a></span>

</span>
</div>
<script src="../js/jquery-3.6.0.min.js"></script>
<script>var base_url = "..";</script>
<script src="../js/theme_extra.js"></script>
<script src="../js/theme.js"></script>
<script src="../search/main.js"></script>
<script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>

</body>
</html>
Loading

0 comments on commit ee7ab41

Please sign in to comment.