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ucscbrowser_mouse.html
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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>Mouse NeoCortex Track Hub for UCSC Genome Browser</title>
<script src="site_libs/header-attrs-2.19/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.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>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
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code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
<style type="text/css">
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
</style>
<style type="text/css">code{white-space: pre;}</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
if (document.readyState && document.readyState === "complete") {
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
}
}
</script>
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
img {
max-width:100%;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
summary {
display: list-item;
}
details > summary > p:only-child {
display: inline;
}
pre code {
padding: 0;
}
</style>
<style type="text/css">
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
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margin-top: 5px;
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.dropdown-submenu:hover>a:after {
border-left-color: #adb5bd;
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.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</style>
<script type="text/javascript">
// manage active state of menu based on current page
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// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
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style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "\e259";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
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content: "\e258";
font-family: 'Glyphicons Halflings';
border: none;
}
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display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
</head>
<body>
<div class="container-fluid main-container">
<div class="navbar navbar-inverse navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-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">scBrainAtlas</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-dna"></span>
UCSC Track Hub
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="ucscbrowser_mouse.html">Mouse</a>
</li>
<li>
<a href="ucscbrowser_human.html">Human</a>
</li>
</ul>
</li>
<li>
<a href="dolphinsuite.html">
<span class="fa fa-laptop"></span>
DolphinSuite
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-project-diagram"></span>
Cellxgene Browser
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cellxgenebrowser.html">Mouse</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-envelope-o"></span>
Contact
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="https://www.umassmed.edu/gtc/about/faculty-publications/miguel-sena-esteves/">Esteves Lab</a>
</li>
<li>
<a href="https://www.umassmed.edu/biocore/">UMass Chan Med. Bioinformatics Core</a>
</li>
<li>
<a href="https://alleninstitute.org/">Allen Institute for Brain Science</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-github"></span>
GitHub
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="https://github.com/UMMS-Biocore/dolphinnext">DolphinNext</a>
</li>
<li>
<a href="https://github.com/UMMS-Biocore/dmeta">DolphinMeta</a>
</li>
<li>
<a href="https://github.com/UMMS-Biocore/dportal">DolphinPortal</a>
</li>
</ul>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div id="header">
<h1 class="title toc-ignore">Mouse NeoCortex Track Hub for UCSC Genome
Browser</h1>
</div>
<style>
table, th, td {
border: 1px solid black;
border-collapse: collapse;
}
body {
text-align: justify}
.main-container {
max-width: 1850px;
margin-left: auto;
margin-right: auto;
}
h1, h2, h3 {
text-align: center;
}
</style>
<!-- ### Count Data -->
<!-- ```{r echo=FALSE, include=FALSE} -->
<!-- knitr::opts_chunk$set(warning = FALSE, message = FALSE) -->
<!-- library(DT) -->
<!-- library(knitr) -->
<!-- datax_rna <- read.table("files/rna_feature_metadata_mouse.tsv", header = T, sep = "\t", row.names = NULL) -->
<!-- datax_atac <- read.table("files/atac_feature_metadata_mouse.tsv", header = T, sep = "\t", row.names = NULL) -->
<!-- datax_cage <- read.table("files/cage_feature_metadata_mouse.tsv", header = T, sep = "\t", row.names = NULL) -->
<!-- ``` -->
<!-- #### **RNA-Seq** -->
<!-- <div align="center"> -->
<!-- ``` {r fig1, echo = FALSE, include=TRUE} -->
<!-- DT::datatable(datax_rna, class = 'display responsive nowrap', filter = 'top', options = list(scrollX = TRUE), rownames = FALSE) -->
<!-- ``` -->
<!-- </div> -->
<!-- #### **ATAC-Seq** -->
<!-- <div align="center"> -->
<!-- ``` {r fig2, echo = FALSE, include=TRUE} -->
<!-- DT::datatable(datax_atac, class = 'display responsive nowrap', filter = 'top', options = list(scrollX = TRUE), rownames = FALSE) -->
<!-- ``` -->
<!-- </div> -->
<!-- #### **CAGE-Seq** -->
<!-- <div align="center"> -->
<!-- ``` {r fig3, echo = FALSE, include=TRUE} -->
<!-- DT::datatable(datax_cage, class = 'display responsive nowrap', filter = 'top', options = list(scrollX = TRUE), rownames = FALSE) -->
<!-- ``` -->
<!-- </div> -->
<!-- ### Genome Browser -->
<!-- <div align="center"> -->
<!-- <iframe width='1850px' height='1000px' frameBorder='0' src='https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr18%3A15393391%2D15410982&hgsid=1402705023_aKIR7wgaDGxjpAodVTAk7KXf1wpp'> -->
<!-- <p>Your browser does not support iframes</p> -->
<!-- </iframe> -->
<!-- </div> -->
<p> This track hub was built by aggregated
<strong>scRNA-Seq</strong>, <strong>scATAC-Seq</strong> and
<strong>CAGE-Seq</strong> reads of the mouse neocortex. You can query
for positions, isoforms and genes to browse sequencing reads and
ATAC-Seq and CAGE-Seq peaks.</p>
<p> In order to download nucleotide sequences, simply
go to <strong>View</strong> -> <strong>DNA</strong> -> <strong>get
DNA</strong>.</p>
<p> See the <a
href="https://dnext.dolphinnext.com/index.php?np=3&id=265">DolphinNext</a>
run for querying genes of interests on an aggregated gene expression and
peaks data table, integrated to this UCSC Track Hub. Click to
<strong>Report</strong> -> <strong>UCSC Genome Browser</strong>.</p>
<p> Please wait until the UCSC Genome Browser is fully
loaded!</p>
<div align="center">
<iframe width='1650px' height='1000px' frameBorder='0' src='https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr18%3A15393391%2D15410982&hgsid=1537661975_iXiaJ28aYWDv7maWuCls6WIhFXZj'>
<p>
Your browser does not support iframes
</p>
<p></iframe></p>
</div>
</div>
<script>
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<script>
$(document).ready(function () {
window.buildTabsets("TOC");
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