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2 changes: 1 addition & 1 deletion docs/_build_html/.buildinfo
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: d1071f1a259f089e911f08368077683e
config: 3be1c78edca01106f3e43cd464c2ff8c
tags: 645f666f9bcd5a90fca523b33c5a78b7
6 changes: 4 additions & 2 deletions docs/_build_html/app_integration.html
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<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="case_studies.html">Case Studies and Tutorials</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer2.html">Clustergrammer2</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_web.html">Clustergrammer-Web</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer2.html">Clustergrammer2 Widget</a></li>
<li class="toctree-l1"><a class="reference internal" href="interacting_with_viz.html">Interacting with the Visualization</a></li>
<li class="toctree-l1"><a class="reference internal" href="biology_specific_features.html">Biology-Specific Features</a></li>
<li class="toctree-l1"><a class="reference internal" href="matrix_format_io.html">Matrix Formats and Input/Output</a></li>
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<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
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24 changes: 14 additions & 10 deletions docs/_build_html/biology_specific_features.html
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<link rel="stylesheet" href="https://unpkg.com/font-awesome@4.5.0/css/font-awesome.min.css" type="text/css" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Case Studies and Examples" href="case_studies.html" />
<link rel="next" title="Matrix Formats and Input/Output" href="matrix_format_io.html" />
<link rel="prev" title="Interacting with the Visualization" href="interacting_with_viz.html" />


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<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_web.html">Clustergrammer Web App</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_widget.html">Clustergrammer Jupyter Widget</a></li>
<li class="toctree-l1"><a class="reference internal" href="case_studies.html">Case Studies and Tutorials</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer2.html">Clustergrammer2</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_web.html">Clustergrammer-Web</a></li>
<li class="toctree-l1"><a class="reference internal" href="interacting_with_viz.html">Interacting with the Visualization</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Biology-Specific Features</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#mouseover-gene-name-and-description">Mouseover Gene Name and Description</a></li>
<li class="toctree-l2"><a class="reference internal" href="#enrichment-analysis">Enrichment Analysis</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="case_studies.html">Case Studies and Examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="matrix_format_io.html">Matrix Formats and Input/Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="building_webpage.html">Web-Development with Clustergrammer</a></li>
<li class="toctree-l1"><a class="reference internal" href="building_webpage.html">Web-Development</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_widget.html">Clustergrammer-Widget</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_js.html">Clustergrammer-JS</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_gl.html">Clustergrammer-GL</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_py.html">Clustergrammer-PY</a></li>
<li class="toctree-l1"><a class="reference internal" href="app_integration.html">App Integration Examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="developing_with_clustergrammer.html">Developing Clustergrammer</a></li>
<li class="toctree-l1"><a class="reference internal" href="app_integration.html">App Integrations</a></li>
<li class="toctree-l1"><a class="reference internal" href="developing_with_clustergrammer.html">Developing</a></li>
<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
</ul>

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<div class="section" id="biology-specific-features">
<span id="id1"></span><h1>Biology-Specific Features<a class="headerlink" href="#biology-specific-features" title="Permalink to this headline"></a></h1>
<p>Clustergrammer was developed to visualize high-dimensional biological data (e.g. genome-wide expression data), but it can also generally be applied to any high-dimensional data. Clustergrammer has several biology-specific features that facilitate the analysis of gene-level biological data, such as: gene expression data, proteomics-data, etc. To take advantage of these features, row names must be official gene names. See the <a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/CCLE/">CCLE Explorer</a> for examples of visualizing gene expression data. These optional biology-specific features are available in the <a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a> as well as the <a class="reference internal" href="clustergrammer_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer Jupyter Widget</span></a> and will automatically activate if the row-names are genes.</p>
<p>Clustergrammer was developed to visualize high-dimensional biological data (e.g. genome-wide expression data), but it can also generally be applied to any high-dimensional data. Clustergrammer has several biology-specific features that facilitate the analysis of gene-level biological data, such as: gene expression data, proteomics-data, etc. To take advantage of these features, row names must be official gene names. See the <a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/CCLE/">CCLE Explorer</a> for examples of visualizing gene expression data. These optional biology-specific features are available in the <a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer-Web</span></a> as well as the <a class="reference internal" href="clustergrammer_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer-Widget</span></a> and will automatically activate if the row-names are genes.</p>
<div class="section" id="mouseover-gene-name-and-description">
<span id="hzome-gene-info"></span><h2>Mouseover Gene Name and Description<a class="headerlink" href="#mouseover-gene-name-and-description" title="Permalink to this headline"></a></h2>
<p>The human genome consists of over 20,000 genes and modern high-throughput measurements are capable of making measurements across the entire genome (e.g. genome-wide expression studies). Human genes have official gene symbols (e.g. <em>EGFR</em>) that are frequently used to label genes in these datasets. Since no biologist can be knowledgeable about every gene in the genome a common and repetitive task is looking up the names and descriptions of genes in a dataset or visualization. To streamline this activity, Clustergrammer automatically displays the full name and description of a gene (provided by data aggregated through the <a class="reference external" href="http://amp.pharm.mssm.edu/Harmonizome/">Harmonizome</a>) as a tooltip when a user mouses over a gene label (see screenshot below). This simple feature speeds up analysis of large gene-level datasets.</p>
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<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">

<a href="case_studies.html" class="btn btn-neutral float-right" title="Case Studies and Examples" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="matrix_format_io.html" class="btn btn-neutral float-right" title="Matrix Formats and Input/Output" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>


<a href="interacting_with_viz.html" class="btn btn-neutral" title="Interacting with the Visualization" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
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<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
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<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="case_studies.html">Case Studies and Tutorials</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer2.html">Clustergrammer2</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_web.html">Clustergrammer-Web</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer2.html">Clustergrammer2 Widget</a></li>
<li class="toctree-l1"><a class="reference internal" href="interacting_with_viz.html">Interacting with the Visualization</a></li>
<li class="toctree-l1"><a class="reference internal" href="biology_specific_features.html">Biology-Specific Features</a></li>
<li class="toctree-l1"><a class="reference internal" href="matrix_format_io.html">Matrix Formats and Input/Output</a></li>
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<li class="toctree-l1"><a class="reference internal" href="clustergrammer_js.html">Clustergrammer-JS</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_gl.html">Clustergrammer-GL</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_py.html">Clustergrammer-PY</a></li>
<li class="toctree-l1"><a class="reference internal" href="app_integration.html">App Integration Examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="developing_with_clustergrammer.html">Developing Clustergrammer</a></li>
<li class="toctree-l1"><a class="reference internal" href="app_integration.html">App Integrations</a></li>
<li class="toctree-l1"><a class="reference internal" href="developing_with_clustergrammer.html">Developing</a></li>
<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
</ul>

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<div class="section" id="web-development">
<span id="building-web-page"></span><h1>Web-Development<a class="headerlink" href="#web-development" title="Permalink to this headline"></a></h1>
<p>Clustergrammer can be used by developers to add interactive heatmap visualizations to their web pages and web applications (see <a class="reference internal" href="app_integration.html#app-integration"><span class="std std-ref">App Integration Examples</span></a>).</p>
<p>Clustergrammer can be used by developers to add interactive heatmap visualizations to their web pages and web applications (see <a class="reference internal" href="app_integration.html#app-integration"><span class="std std-ref">App Integrations</span></a>).</p>
<div class="section" id="embedding-clustergrammer">
<h2>Embedding Clustergrammer<a class="headerlink" href="#embedding-clustergrammer" title="Permalink to this headline"></a></h2>
<p>The Clustergrammer web app can be used to produce visualizations that are embedded into another page using an IFrame; see below:</p>
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<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script type="text/javascript" src="https://unpkg.com/@jupyter-widgets/html-manager@^0.14.0/dist/embed-amd.js"></script>
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<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script type="text/javascript" src="https://unpkg.com/@jupyter-widgets/html-manager@^0.14.0/dist/embed-amd.js"></script>
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<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_web.html">Clustergrammer Web App</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_widget.html">Clustergrammer-Widget</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer2.html">Clustergrammer2 Widget</a></li>
<li class="toctree-l1"><a class="reference internal" href="case_studies.html">Case Studies and Tutorials</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer2.html">Clustergrammer2</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_web.html">Clustergrammer-Web</a></li>
<li class="toctree-l1"><a class="reference internal" href="interacting_with_viz.html">Interacting with the Visualization</a></li>
<li class="toctree-l1"><a class="reference internal" href="biology_specific_features.html">Biology-Specific Features</a></li>
<li class="toctree-l1"><a class="reference internal" href="case_studies.html">Case Studies and Examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="matrix_format_io.html">Matrix Formats and Input/Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="building_webpage.html">Web-Development with Clustergrammer</a></li>
<li class="toctree-l1"><a class="reference internal" href="building_webpage.html">Web-Development</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_widget.html">Clustergrammer-Widget</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_js.html">Clustergrammer-JS</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Clustergrammer-GL</a></li>
<li class="toctree-l1"><a class="reference internal" href="clustergrammer_py.html">Clustergrammer-PY</a></li>
<li class="toctree-l1"><a class="reference internal" href="app_integration.html">App Integration Examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="developing_with_clustergrammer.html">Developing Clustergrammer</a></li>
<li class="toctree-l1"><a class="reference internal" href="app_integration.html">App Integrations</a></li>
<li class="toctree-l1"><a class="reference internal" href="developing_with_clustergrammer.html">Developing</a></li>
<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
</ul>

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<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script type="text/javascript" src="https://unpkg.com/@jupyter-widgets/html-manager@^0.14.0/dist/embed-amd.js"></script>
<script type="text/javascript" src="https://unpkg.com/@jupyter-widgets/html-manager@^0.18.0/dist/embed-amd.js"></script>



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