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<!DOCTYPE html>
<html class="no-js" lang="en-US" xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en-us">
<head>
<meta name="generator" content="Hugo 0.80.0" />
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="Epiviz">
<meta name="author" content="epiviz">
<meta name="keyword" content="">
<link rel="shortcut icon" href="https://epiviz.github.io/favicon.ico">
<script src="https://epiviz.github.io/polymer/charts/components/webcomponentsjs/webcomponents-lite.js"></script>
<title>Epiviz</title>
<link rel="import" href="https://epiviz.github.io/polymer/charts/components/epiviz-data-source/epiviz-data-source.html">
<link rel="import" href="https://epiviz.github.io/polymer/charts/components/epiviz-charts/epiviz-charts.html">
<link rel="stylesheet" href="https://epiviz.github.io/css/theme/simplex.css">
<link rel="stylesheet" href="https://epiviz.github.io/css/font-awesome.min.css">
<link rel="stylesheet" href="https://epiviz.github.io/css/style.css">
<script src="https://epiviz.github.io/js/jquery.min-2.1.4.js"></script>
<script src="https://epiviz.github.io/js/bootstrap.min-3.3.5.js"></script>
<link href="https://epiviz.github.io/index.xml" rel="alternate" type="application/rss+xml" title="Epiviz" />
</head>
<body lang="en-US">
<div class="container">
<div class="row">
<div class="navbar navbar-default " role="navigation">
<div class="navbar-header">
<a class="navbar-brand" href="https://epiviz.github.io"><img src="https://epiviz.github.io/images/epiviz_4_logo_medium.png"></a>
</div>
<div class="navbar-collapse collapse navbar-responsive-collapse">
<ul class="nav navbar-nav navbar-right">
<li><a href="https://epiviz.github.io">Home</a></li>
<li><a href="https://epiviz.github.io/post/">News</a></li>
<li><a href="https://epiviz.github.io/metaviz/"> Metaviz </a></li>
<li><a href="https://epiviz.github.io/tutorials/"> Tutorials </a></li>
<li><a href="https://epiviz.github.io/documentation/"> Documentation </a></li>
<li><a href="https://epiviz.github.io/contact/"> Contact Us </a></li>
</ul>
</div>
</div>
</div>
</div>
<div class="container">
<div class="row">
<div class="col-md-9 col-md-offset-1">
<p>
Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome
browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps
and other user-supplied visualizations. It also includes data from the
<a target="_blank" href="http://barcode.luhs.org/">Gene Expression Barcode project</a>
for transcriptome visualization. It has a flexible plugin framework so users can add
<a target="_blank" href="http://d3js.org/">d3</a> visualizations. You can see a video tour
<a target="_blank" href="http://youtu.be/099c4wUxozA">here</a>.
</p>
<p style="text-align: center;">
<iframe width="480" height="360" src="https://www.youtube.com/embed/099c4wUxozA" frameborder="0"></iframe>
</p>
<p>
The
<a target="_blank" href="http://bioconductor.org/packages/release/bioc/html/epivizr.html">Epivizr Bioconductor package</a>
implements two-way communication between the
<code>R/Bioconductor</code> computational genomics environment and Epiviz. Objects in an
<code>R</code> session can be displayed as tracks or plots on Epiviz. Epivizr uses
<a target="_blank" href="http://www.websocket.org/">WebSockets</a> for communication between the browser
<code>JavaScript</code> client and the
<code>R</code> environment, the same technology underlying the popular
<a target="_blank" href="http://www.rstudio.com/shiny/">Shiny</a> system for authoring interactive web-based reports in
<code>R</code>.
</p>
</div>
</div>
<h3>Applications</h3>
<div class="row">
<div class="col-md-12">
<hr>
</div>
</div>
<div class="row">
<div class="col-sm-6 col-md-3">
<div class="thumbnail">
<img src="images/epiviz.jpg" alt="Epiviz" />
<div class="caption">
<h3>Epiviz Feed</h3>
<p>Epiviz Feed combines interactive visualization of genomic data with proactive statistical analyses.</p>
<p>
<a href="http://54.157.53.251/browser/" target="_blank" class="btn btn-primary" role="button">Website</a>
<a href="https://github.com/epiviz/epiviz-feed-computation" target="_blank" class="btn btn-primary" role="button">Github</a>
</p>
</div>
</div>
</div>
<div class="col-sm-6 col-md-3">
<div class="thumbnail">
<img src="images/epiviz.jpg" alt="Epiviz" />
<div class="caption">
<h3>Epiviz</h3>
<p>Epiviz is an interactive exploratory and visualization tool for functional genomics data</p>
<p>
<a href="http://epiviz.cbcb.umd.edu/4/?ws=Ago25FdPLVb&seqName=chr2&start=69300680&end=90699322" target="_blank" class="btn btn-primary" role="button">Website</a>
<a href="https://github.com/epiviz/epiviz" target="_blank" class="btn btn-primary" role="button">Github</a>
</p>
</div>
</div>
</div>
<div class="col-sm-6 col-md-3">
<div class="thumbnail">
<img src="images/metaviz.png" alt="metaviz" />
<div class="caption">
<h3>Metaviz</h3>
<p>Metaviz is an interactive visualization tool for 16S metagenomics datasets using a novel visualization to navigate taxonomic hierarchies</p>
<p>
<a href="http://metaviz.cbcb.umd.edu/?ws=yA4BWgUOTiq" target="_blank" class="btn btn-primary" role="button">Website</a>
<a href="https://github.com/epiviz/epiviz" target="_blank" class="btn btn-primary" role="button">Github</a>
</p>
</div>
</div>
</div>
<div class="col-sm-6 col-md-3">
<div class="thumbnail">
<img src="images/epiviz_desktop.png" alt="epiviz desktop " />
<div class="caption">
<h3>Epiviz Desktop</h3>
<p>Desktop application for the epiviz genomics data browser. Also supports visualization of local datasets through epivizR package.</p>
<p>
<a href="https://github.com/epiviz/epiviz-desktop-app/releases" target="_blank" class="btn btn-primary" role="button">Download</a>
<a href="https://github.com/epiviz/epiviz-desktop-app" target="_blank" class="btn btn-primary" role="button">Github</a>
</p>
</div>
</div>
</div>
</div>
<h3>Tools and Packages </h3>
<div class="row">
<div class="col-md-12">
<hr>
</div>
</div>
<div class="row">
<div class="col-sm-6 col-md-4">
<div class="thumbnail">
<div class="caption">
<h3>Epiviz File Server</h3>
<p>Query, Transform and Visualize genomic data directly from indexed files formats.</p>
<p>
<a href="https://github.com/epiviz/epivizFileParser" target="_blank" class="btn btn-primary" role="button">Github</a>
<a href="https://epivizfileparser.readthedocs.io/en/latest/" target="_blank" class="btn btn-primary" role="button">Docs</a>
</p>
</div>
</div>
</div>
<div class="col-sm-6 col-md-4">
<div class="thumbnail">
<div class="caption">
<h3>epivizR</h3>
<p>epivizR is an R/Bioconductor package that handles genomic data from R session to the epiviz app.</p>
<p>
<a href="https://github.com/epiviz/epivizr" target="_blank" class="btn btn-primary" role="button">Github</a>
<a href="http://bioconductor.org/packages/release/bioc/html/epivizr.html" target="_blank" class="btn btn-primary" role="button">Bioconductor</a>
<a href="" target="_blank" class="btn btn-primary" role="button">Docs</a>
</p>
</div>
</div>
</div>
<div class="col-sm-6 col-md-4">
<div class="thumbnail">
<div class="caption">
<h3>Epiviz Web Components</h3>
<p>Epiviz Components are extensible and reusable HTML elements to visualize genomic data.</p>
<p>
<a href="https://github.com/epiviz/epiviz-chart" target="_blank" class="btn btn-primary" role="button">Github</a>
<a href="https://epiviz.github.io/documentation/" target="_blank" class="btn btn-primary" role="button">Docs</a>
</p>
</div>
</div>
</div>
<div class="col-sm-6 col-md-4">
<div class="thumbnail">
<div class="caption">
<h3>metavizR</h3>
<p>metavizR is an R package that handles metagenomics datasets from an R session to the metaviz app.</p>
<p>
<a href="https://github.com/epiviz/metavizr" target="_blank" class="btn btn-primary" role="button">Github</a>
<a href="" target="_blank" class="btn btn-primary" role="button">Docs</a>
</p>
</div>
</div>
</div>
<div class="col-sm-6 col-md-4">
<div class="thumbnail">
<div class="caption">
<h3>epivizrData</h3>
<p>epivizrData manages various bioconductor data types and makes them available to the epivizR and the epiviz app.</p>
<p>
<a href="https://github.com/epiviz/epivizrData" target="_blank" class="btn btn-primary" role="button">Github</a>
<a href="http://bioconductor.org/packages/release/bioc/html/epivizrData.html" target="_blank" class="btn btn-primary" role="button">Bioconductor</a>
<a href="" target="_blank" class="btn btn-primary" role="button">Docs</a>
</p>
</div>
</div>
</div>
<div class="col-sm-6 col-md-4">
<div class="thumbnail">
<div class="caption">
<h3>epivizrServer</h3>
<p>epivizrServer is a server management package that creates and manages the websocket session between R and epiviz app.</p>
<p>
<a href="https://github.com/epiviz/epivizrServer" target="_blank" class="btn btn-primary" role="button">Github</a>
<a href="http://bioconductor.org/packages/release/bioc/html/epivizrServer.html" target="_blank" class="btn btn-primary" role="button">Bioconductor</a>
<a href="" target="_blank" class="btn btn-primary" role="button">Docs</a>
</p>
</div>
</div>
</div>
</div>
<h3>Publications</h3>
<div class="row">
<div class="col-md-12">
<hr>
</div>
</div>
<div class="row">
<ul>
<li>Kancherla J, Yang Y, Chae H and Bravo HC. (2020) Epiviz File Server: Query, Transform and Interactively Explore Data from Indexed Genomic Files.
<a href="https://doi.org/10.1093/bioinformatics/btaa591">Oxford Bioinformatics</a>
</li>
<li>Cui Z, Kancherla J, Zhang A, Bravo HC. Elmqvist N (2019) Sherpa: Leveraging User Attention for Computational Steering in Visual Analytics.
<a href="https://doi.org/10.1109/VDS48975.2019.8973384">IEEE VDS</a>
</li>
<li>Cui Z, Kancherla J, Chang K, Elmqvist N and Bravo HC. (2019) Proactive visual and statistical analysis of genomic data in Epiviz.
<a href="https://dx.doi.org/10.1093/bioinformatics/btz883">Oxford Bioinformatics</a>
</li>
<li>Wagner, J., Chelaru, F., Kancherla, J., Paulson, JN., Felix, V., Mahurkar, A., Corrada Bravo, H. (2018). “Metaviz: interactive statistical and visual analysis of metagenomic data”.
<a href="https://doi.org/10.1093/nar/gky136">Nucleic Acids Research</a>
</li>
<li>Chelaru, F., Corrada Bravo H. (2015). “Epiviz: a view inside the design of an integrated visual analysis software for genomics”. BMC Bioinformatics 16 (Suppl 11):S4.
<a href="http://www.biomedcentral.com/1471-2105/16/S11/S4">BMC Bioinformatics</a>
</li>
<li>Chelaru, F., Smith, L., Goldstein, N., Corrada Bravo, H. (2014). “Epiviz: interactive visual analytics for functional genomics data”. Nature Methods 11, 938-940.
<a href="http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3038.html">Nature Methods</a>
</li>
</ul>
</div>
<div class="row">
<div class="col-md-12">
<hr>
</div>
</div>
</div>
<div class="container">
<div class="row col-md-12">
<footer>
<div class="pull-left">
<p>
© 2012 ~ University of Maryland, Hector Corrada Bravo, Jayaram Kancherla, Florin Chelaru. All Rights Reserved ~ Powered By <a href="http://hugo.spf13.com">Hugo</a> - version: 0.80.0 ~ <a href="https://epiviz.github.io/license">License</a>
</p>
</div>
<div class="pull-right">
<a href="https://twitter.com/epiviz" target="_blank">
<i class="fa fa-twitter-square fa-2x"></i></a>
<a href="https://github.com/epiviz" target="_blank">
<i class="fa fa-github-square fa-2x"></i></a>
<a href="https://epiviz.github.io/index.xml" target="_blank">
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