csinva
/
auxilin-prediction
mirror of https://github.com/Yu-Group/auxilin-prediction


  
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<title>src API documentation</title>
<meta name="description" content="Python package for documenting all the functions used in auxilin prediction.
predicting auxilin spikes in clathrin-mediated endocytosis …" />
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</head>
<body>
<main>
<article id="content">
<header>
<h1 class="title">Module <code>src</code></h1>
</header>
<section id="section-intro">
<p>Python package for documenting all the functions used in auxilin prediction.</p>
<h1 id="predicting-auxilin-spikes-in-clathrin-mediated-endocytosis">predicting auxilin spikes in clathrin-mediated endocytosis</h1>
<p><img alt="" src="https://yu-group.github.io/auxilin-prediction/fig_pipeline.jpg"></p>
<h2 id="quickstart-for-making-new-predictions">quickstart for making new predictions</h2>
<ul>
<li>our fully trained model is available in the <a href="models">models</a> folder</li>
</ul>
<h2 id="reproducibility">reproducibility</h2>
<ul>
<li><strong>download data</strong>: download cached data after tracking from <a href="https://drive.google.com/drive/folders/1mh2wn0KLtj90j_rfgPUGEJgMZAEl0Yi7?usp=sharing">this gdrive folder</a> - should be added to the folder <code>data/tracks</code></li>
<li><strong>process data</strong>: run <code>python data.py</code> to properly preprocess all the data (will cache it into the "processed folder")</li>
<li><strong>rerun analysis</strong>: <a href="notebooks">notebooks</a> folder contains step-by-step analysis</li>
<li><strong>tests</strong>: run tests with <code>pytest</code> in the <code>tests</code> folder</li>
</ul>
<h2 id="acknowledgements">acknowledgements</h2>
<ul>
<li>this is a collaboration between the Berkeley <a href="https://www.stat.berkeley.edu/~yugroup/">Yu-Group</a> and the <a href="http://abc.berkeley.edu/">Berkeley Advanced Bioimaging Center</a></li>
<li>uses code from several wonderful packages including <a href="https://github.com/DanuserLab/cmeAnalysis">cmeAnalysis</a> (DanuserLab)</li>
</ul>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">&#34;&#34;&#34;
Python package for documenting all the functions used in auxilin prediction.
.. include:: ../readme.md
&#34;&#34;&#34;</code></pre>
</details>
</section>
<section>
<h2 class="section-title" id="header-submodules">Sub-modules</h2>
<dl>
<dt><code class="name"><a title="src.analyze_helper" href="analyze_helper.html">src.analyze_helper</a></code></dt>
<dd>
<section class="desc"></section>
</dd>
<dt><code class="name"><a title="src.config" href="config.html">src.config</a></code></dt>
<dd>
<section class="desc"><p>Set configurations for all the raw and processed datasets
Takes in path to raw data, tracks, processed df, and then later interim data</p></section>
</dd>
<dt><code class="name"><a title="src.data" href="data.html">src.data</a></code></dt>
<dd>
<section class="desc"></section>
</dd>
<dt><code class="name"><a title="src.features" href="features.html">src.features</a></code></dt>
<dd>
<section class="desc"></section>
</dd>
<dt><code class="name"><a title="src.interpret" href="interpret.html">src.interpret</a></code></dt>
<dd>
<section class="desc"></section>
</dd>
<dt><code class="name"><a title="src.load_tracking" href="load_tracking.html">src.load_tracking</a></code></dt>
<dd>
<section class="desc"></section>
</dd>
<dt><code class="name"><a title="src.models" href="models.html">src.models</a></code></dt>
<dd>
<section class="desc"></section>
</dd>
<dt><code class="name"><a title="src.neural_networks" href="neural_networks.html">src.neural_networks</a></code></dt>
<dd>
<section class="desc"></section>
</dd>
<dt><code class="name"><a title="src.outcomes" href="outcomes.html">src.outcomes</a></code></dt>
<dd>
<section class="desc"></section>
</dd>
<dt><code class="name"><a title="src.ref" href="ref/index.html">src.ref</a></code></dt>
<dd>
<section class="desc"></section>
</dd>
<dt><code class="name"><a title="src.train" href="train.html">src.train</a></code></dt>
<dd>
<section class="desc"></section>
</dd>
<dt><code class="name"><a title="src.train_reg" href="train_reg.html">src.train_reg</a></code></dt>
<dd>
<section class="desc"></section>
</dd>
<dt><code class="name"><a title="src.trend_filtering" href="trend_filtering.html">src.trend_filtering</a></code></dt>
<dd>
<section class="desc"></section>
</dd>
<dt><code class="name"><a title="src.viz" href="viz.html">src.viz</a></code></dt>
<dd>
<section class="desc"></section>
</dd>
</dl>
</section>
<section>
</section>
<section>
</section>
<section>
</section>
</article>
<nav id="sidebar">
<h1>Index</h1>
<div class="toc">
<ul>
<li><a href="#predicting-auxilin-spikes-in-clathrin-mediated-endocytosis">predicting auxilin spikes in clathrin-mediated endocytosis</a><ul>
<li><a href="#quickstart-for-making-new-predictions">quickstart for making new predictions</a></li>
<li><a href="#reproducibility">reproducibility</a></li>
<li><a href="#acknowledgements">acknowledgements</a></li>
</ul>
</li>
</ul>
</div>
<ul id="index">
<li><h3><a href="#header-submodules">Sub-modules</a></h3>
<ul>
<li><code><a title="src.analyze_helper" href="analyze_helper.html">src.analyze_helper</a></code></li>
<li><code><a title="src.config" href="config.html">src.config</a></code></li>
<li><code><a title="src.data" href="data.html">src.data</a></code></li>
<li><code><a title="src.features" href="features.html">src.features</a></code></li>
<li><code><a title="src.interpret" href="interpret.html">src.interpret</a></code></li>
<li><code><a title="src.load_tracking" href="load_tracking.html">src.load_tracking</a></code></li>
<li><code><a title="src.models" href="models.html">src.models</a></code></li>
<li><code><a title="src.neural_networks" href="neural_networks.html">src.neural_networks</a></code></li>
<li><code><a title="src.outcomes" href="outcomes.html">src.outcomes</a></code></li>
<li><code><a title="src.ref" href="ref/index.html">src.ref</a></code></li>
<li><code><a title="src.train" href="train.html">src.train</a></code></li>
<li><code><a title="src.train_reg" href="train_reg.html">src.train_reg</a></code></li>
<li><code><a title="src.trend_filtering" href="trend_filtering.html">src.trend_filtering</a></code></li>
<li><code><a title="src.viz" href="viz.html">src.viz</a></code></li>
</ul>
</li>
</ul>
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