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+config: 85df347c4f600634fe327234c581008e
+tags: 645f666f9bcd5a90fca523b33c5a78b7
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+<!DOCTYPE html>
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+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Overview: module code &mdash; momics</title>
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+        <div class="wy-side-nav-search" >
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+          <a href="../index.html" class="icon icon-home">
+            momics
+              <img src="../_static/logo.svg" class="logo" alt="Logo"/>
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/intro.html">What is <code class="docutils literal notranslate"><span class="pre">momics</span></code>?</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/intro.html#a-file-format-for-efficient-storage-of-multi-omics-data">A file format for efficient storage of multi-omics data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/intro.html#a-large-scale-multi-omics-data-management-framework">A large-scale multi-omics data management framework</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/intro.html#an-efficient-query-engine-for-multi-omics-data">An efficient query engine for multi-omics data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/intro.html#an-integration-layer-of-multi-omics-data-and-machine-learning">An integration layer of multi-omics data and machine learning</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/concepts.html">Concepts</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/concepts.html#id1"></a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/get-started.html">Get started with <code class="docutils literal notranslate"><span class="pre">momics</span></code></a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/get-started.html#installation">Installation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/get-started.html#quick-start">Quick start</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/get-started.html#going-further">Going further</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/api.html">Introduction to <code class="docutils literal notranslate"><span class="pre">momics</span></code> API</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/api.html#creating-momics-repositories">Creating <code class="docutils literal notranslate"><span class="pre">momics</span></code> repositories</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/api.html#registering-chromosomes">Registering chromosomes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/api.html#populating-momics-repositories">Populating <code class="docutils literal notranslate"><span class="pre">momics</span></code> repositories</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/api.html#querying-momics-repositories">Querying <code class="docutils literal notranslate"><span class="pre">momics</span></code> repositories</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../user_guide/api.html#registering-a-query">Registering a query</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../user_guide/api.html#running-a-query">Running a query</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../user_guide/api.html#exporting-query-results">Exporting query results</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/api.html#going-further">Going further</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/cli.html">Introduction to <code class="docutils literal notranslate"><span class="pre">momics</span></code> CLI</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/cli.html#basic-cli-usage">Basic CLI usage</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/cli.html#extra-cli-utilities">Extra CLI utilities</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_guide/cli.html#going-further">Going further</a></li>
+</ul>
+</li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Tutorials</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../tutorials/integrating-multiomics.html">Integrating multi-omics data with <code class="docutils literal notranslate"><span class="pre">momics</span></code></a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/integrating-multiomics.html#Creating-a-local-momics-repository">Creating a local <code class="docutils literal notranslate"><span class="pre">momics</span></code> repository</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../tutorials/cloud-repos.html">Managing cloud-hosted <code class="docutils literal notranslate"><span class="pre">momics</span></code> repositories</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/cloud-repos.html#Prerequisites">Prerequisites</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/cloud-repos.html#Creating-a-momics-repository-on-an-S3-bucket">Creating a <code class="docutils literal notranslate"><span class="pre">momics</span></code> repository on an S3 bucket</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/cloud-repos.html#Adding-data-to-the-repository">Adding data to the repository</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/cloud-repos.html#Querying-data-from-the-repository">Querying data from the repository</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/cloud-repos.html#Extracting-data-from-the-repository">Extracting data from the repository</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/cloud-repos.html#Deleting-a-repository">Deleting a repository</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../tutorials/nn-training.html">Train neural networks with <code class="docutils literal notranslate"><span class="pre">momics</span></code> and <code class="docutils literal notranslate"><span class="pre">tensorflow</span></code></a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/nn-training.html#Connect-to-the-data">Connect to the data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/nn-training.html#Modify-some-tracks">Modify some tracks</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/nn-training.html#Define-model">Define model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/nn-training.html#Fit-the-model">Fit the model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/nn-training.html#Evaluate-and-save-model">Evaluate and save model</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/nn-training.html#Use-the-model-to-predict-ATAC-seq-coverage">Use the model to predict ATAC-seq coverage</a></li>
+</ul>
+</li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">References</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../api/index.html">API Reference</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../api/momics/index.html">momics</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../api/momics/index.html#submodules">Submodules</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../api/momics/chromnn/index.html">momics.chromnn</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/momics/config/index.html">momics.config</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/momics/dataset/index.html">momics.dataset</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/momics/export/index.html">momics.export</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/momics/logging/index.html">momics.logging</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/momics/momics/index.html">momics.momics</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/momics/momicsquery/index.html">momics.momicsquery</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/momics/streamer/index.html">momics.streamer</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/momics/utils/index.html">momics.utils</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/momics/version/index.html">momics.version</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="../api/momics/index.html#attributes">Attributes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../api/momics/index.html#package-contents">Package Contents</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../api/momics/index.html#momics.__format_version__"><code class="docutils literal notranslate"><span class="pre">__format_version__</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/momics/index.html#momics.__version__"><code class="docutils literal notranslate"><span class="pre">__version__</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../cli/index.html">CLI Reference</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../cli/index.html#contents">Contents</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../cli/index.html#momics">momics</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../cli/index.html#momics-binnify">binnify</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../cli/index.html#momics-config">config</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../cli/index.html#momics-cp">cp</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../cli/index.html#momics-create">create</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../cli/index.html#momics-delete">delete</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../cli/index.html#momics-ingest">ingest</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../cli/index.html#momics-ls">ls</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../cli/index.html#momics-query">query</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../cli/index.html#momics-remove">remove</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../cli/index.html#momics-tree">tree</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
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+          <a href="../index.html">momics</a>
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+      <li class="breadcrumb-item active">Overview: module code</li>
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+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="_thread.html">_thread</a></li>
+<li><a href="momics/chromnn.html">momics.chromnn</a></li>
+<li><a href="momics/config.html">momics.config</a></li>
+<li><a href="momics/dataset.html">momics.dataset</a></li>
+<li><a href="momics/export.html">momics.export</a></li>
+<li><a href="momics/logging.html">momics.logging</a></li>
+<li><a href="momics/momics.html">momics.momics</a></li>
+<li><a href="momics/momicsquery.html">momics.momicsquery</a></li>
+<li><a href="momics/streamer.html">momics.streamer</a></li>
+<li><a href="momics/utils.html">momics.utils</a></li>
+</ul>
+
+           </div>
+          </div>
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+    <p>&#169; Copyright 2023-2024, Jacques Serizay.
+      <span class="lastupdated">Last updated on Oct 21, 2024.
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