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<!DOCTYPE html>
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<title>Tissue Enrichment Analysis (TEA) by dangeles</title>
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<section class="page-header">
<h1 class="project-name">Tissue Enrichment Analysis (TEA)</h1>
<h2 class="project-tagline">This repository holds the scripts for WormBase's tissue enrichment analysis tool (TEA).</h2>
<a href="https://github.com/dangeles/TissueEnrichmentAnalysis" class="btn">View on GitHub</a>
<a href="https://github.com/dangeles/TissueEnrichmentAnalysis/zipball/master" class="btn">Download .zip</a>
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<section class="main-content">
<h1>
<a id="tissue-enrichment-analysis-tea" class="anchor" href="#tissue-enrichment-analysis-tea" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Tissue Enrichment Analysis (TEA)</h1>
<p>This repository holds the scripts to calculate enrichment of a set of labels using hypergeometric statistics. Results are output to a dataframe. A standard plotting function is provided, but it is really just a thin wrapper around a seaborn plot.</p>
<h1>
<a id="requirements" class="anchor" href="#requirements" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Requirements</h1>
<p>This library has been developed in Python >= 3.5, using the Anaconda distribution. Requirements include <code>pandas</code>, <code>matplotlib</code>, <code>numpy</code>, <code>scipy</code> and <code>seaborn</code>.</p>
<h1>
<a id="installation" class="anchor" href="#installation" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Installation</h1>
<p>Use <code>pip install tissue_enrichment_analysis</code></p>
<h1>
<a id="basic-usage" class="anchor" href="#basic-usage" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Basic Usage</h1>
<h2>
<a id="web-usage" class="anchor" href="#web-usage" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Web usage</h2>
<p>Go to <a href="http://www.wormbase.org/tea">www.wormbase.org/tea</a>, input your gene list and enjoy the results!</p>
<h2>
<a id="within-a-python-script" class="anchor" href="#within-a-python-script" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Within a Python Script</h2>
<p>There are really just two main functions that are provided in TEA: <code>enrichment_analysis</code> and <code>plot_enrichment_results</code>.</p>
<p>A standard call to this library would be as follows:</p>
<p><code>import tissue_enrichment_analysis as tea</code></p>
<p><code>gene_list= some_gene_list</code></p>
<p><code>tissue_df= tea.fetch_dictionary()</code></p>
<p><code>df_results= tea.enrichment_analysis(tissue_df, gene_list, aname= 'FileName')</code></p>
<p><code>tea.plot_enrichment_results(df_results, title= 'FileName')</code></p>
<h2>
<a id="calling-from-terminal" class="anchor" href="#calling-from-terminal" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Calling from Terminal</h2>
<p>Gene enrichment analysis can be generated easily by calling the program via terminal using: <code>tea tissue_dictionary your_gene_list -[OPTIONS]</code></p>
<p>Type <code>tea -h</code> for help and full documentation.</p>
<h1>
<a id="future-work" class="anchor" href="#future-work" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Future Work</h1>
<p>We may try to add support for other model organisms!</p>
<h1>
<a id="contact" class="anchor" href="#contact" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Contact</h1>
<p>If you find any bugs, have suggestions or just want to say hi, feel free to contact me at <a href="mailto:dangeles@caltech.edu">dangeles@caltech.edu</a></p>
<p>Good luck!</p>
<p>David Angeles-Albores</p>
<h1>
<a id="author" class="anchor" href="#author" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Author:</h1>
<p>David Angeles-Albores</p>
<h1>
<a id="contributors" class="anchor" href="#contributors" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Contributors:</h1>
<p>Raymond Y. Lee, Paul W. Sternberg</p>
<h1>
<a id="acknowledgements" class="anchor" href="#acknowledgements" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Acknowledgements</h1>
<p>With special thanks to the entire worm community!</p>
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<span class="site-footer-owner"><a href="https://github.com/dangeles/TissueEnrichmentAnalysis">Tissue Enrichment Analysis (TEA)</a> is maintained by <a href="https://github.com/dangeles">dangeles</a>.</span>
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