deploy: e4a244e

.buildinfo

@@ -1,4 +1,4 @@
 # 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: 21c87eaab7628f6b295ee24abc553fc2
+config: b223df3ff4acc957dc19d2abf7451abf
 tags: 645f666f9bcd5a90fca523b33c5a78b7

Readme.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>CLASTER</title>
+    <title>CLASTER &#8212; CLASTER</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=3ee479438cf8b5e0d341" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=3ee479438cf8b5e0d341"></script>
 
-    <script src="_static/documentation_options.js?v=9eb32ce0"></script>
+    <script src="_static/documentation_options.js?v=6771b56e"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=efea14e4"></script>
@@ -131,7 +131,7 @@
 
 
 
-    <p class="title logo__title"></p>
+    <p class="title logo__title">CLASTER</p>
 
 </a></div>
         <div class="sidebar-primary-item"><ul class="navbar-icon-links navbar-nav"
@@ -173,6 +173,14 @@
         <p aria-level="2" class="caption" role="heading"><span class="caption-text">Tutorial:</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="scripts/0_Tutorial.html">TUTORIAL</a></li>
+</ul>
+<p aria-level="2" class="caption" role="heading"><span class="caption-text">Scripts:</span></p>
+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="scripts/1_Data_obtention.html">1. DATA OBTENTION &amp; PREPROCESSING</a></li>
+<li class="toctree-l1"><a class="reference internal" href="scripts/2_Run_CLASTER.html">2. CREATE &amp; RUN CLASTER</a></li>
+<li class="toctree-l1"><a class="reference internal" href="scripts/2b_Run_HyenaDNA_and_Enformer.html">2b. BENCHMARKING CLASTER WITH HYENA-DNA AND ENFORMER</a></li>
+<li class="toctree-l1"><a class="reference internal" href="scripts/3_Data_analysis.html">DATA ANALYSIS NOTEBOOK</a></li>
+
 </ul>
 
     </div>

_sources/index.rst

@@ -13,3 +13,11 @@ Modeling nascent RNA transcription from chromatin landscape and structure
 
     scripts/0_Tutorial.ipynb
 
+.. toctree::
+    :maxdepth: 2
+    :caption: Scripts:
+
+    scripts/1_Data_obtention.ipynb
+    scripts/2_Run_CLASTER.ipynb
+    scripts/2b_Run_HyenaDNA_and_Enformer.ipynb
+    scripts/3_Data_analysis.ipynb

_sources/scripts/0_Tutorial.ipynb

@@ -1635,7 +1635,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.undefined.undefined"
   },
   "orig_nbformat": 4,
   "vscode": {

_sources/scripts/1_Data_obtention.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# <center> 1. DATA OBTENTION & PREPROCESSING <center>\n",
+    "# 1. DATA OBTENTION & PREPROCESSING\n",
     "\n",
     "Hi!\n",
     "This notebook is a guide to obtain and preprocess the data used to train and test CLASTER. It is meant to be run sequentially, i.e. one cell after the other, and it mainly contains:\n",
@@ -18,7 +18,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Before we start ...\n",
+    "## Before we start ...\n",
     "\n",
     "A) It would be highly recommendable to create an environment for this project. The python package EIR, which is the core framework used to build, train and test CLASTER, will need python >= 3.11. If you have anaconda, it can be done as follows from the terminal:\n",
     "\n",
@@ -69,7 +69,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 1. Data obtention"
+    "## 1. Data obtention"
    ]
   },
   {

_sources/scripts/2_Run_CLASTER.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# <center> 2. CREATE & RUN CLASTER <center>"
+    "# 2. CREATE & RUN CLASTER"
    ]
   },
   {

_sources/scripts/2b_Run_HyenaDNA_and_Enformer.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# <center> 2b. BENCHMARKING CLASTER WITH HYENA-DNA AND ENFORMER <center>"
+    "# 2b. BENCHMARKING CLASTER WITH HYENA-DNA AND ENFORMER"
    ]
   },
   {

_sources/scripts/3_Data_analysis.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# <center> DATA ANALYSIS NOTEBOOK <center>\n",
+    "# DATA ANALYSIS NOTEBOOK\n",
     "\n",
     "This notebook was used to run the analyses and produce most of the images in the paper.\n",
     "\n",

_static/documentation_options.js

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '',
+    VERSION: '2024.05.29',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

genindex.html

@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index</title>
+    <title>Index &#8212; CLASTER</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=3ee479438cf8b5e0d341" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=3ee479438cf8b5e0d341"></script>
 
-    <script src="_static/documentation_options.js?v=9eb32ce0"></script>
+    <script src="_static/documentation_options.js?v=6771b56e"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=efea14e4"></script>
@@ -130,7 +130,7 @@
 
 
 
-    <p class="title logo__title"></p>
+    <p class="title logo__title">CLASTER</p>
 
 </a></div>
         <div class="sidebar-primary-item"><ul class="navbar-icon-links navbar-nav"
@@ -172,6 +172,14 @@
         <p aria-level="2" class="caption" role="heading"><span class="caption-text">Tutorial:</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="scripts/0_Tutorial.html">TUTORIAL</a></li>
+</ul>
+<p aria-level="2" class="caption" role="heading"><span class="caption-text">Scripts:</span></p>
+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="scripts/1_Data_obtention.html">1. DATA OBTENTION &amp; PREPROCESSING</a></li>
+<li class="toctree-l1"><a class="reference internal" href="scripts/2_Run_CLASTER.html">2. CREATE &amp; RUN CLASTER</a></li>
+<li class="toctree-l1"><a class="reference internal" href="scripts/2b_Run_HyenaDNA_and_Enformer.html">2b. BENCHMARKING CLASTER WITH HYENA-DNA AND ENFORMER</a></li>
+<li class="toctree-l1"><a class="reference internal" href="scripts/3_Data_analysis.html">DATA ANALYSIS NOTEBOOK</a></li>
+
 </ul>
 
     </div>

index.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Claster</title>
+    <title>Claster &#8212; CLASTER</title>
 
 
 
@@ -37,10 +37,12 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=3ee479438cf8b5e0d341" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=3ee479438cf8b5e0d341"></script>
 
-    <script src="_static/documentation_options.js?v=9eb32ce0"></script>
+    <script src="_static/documentation_options.js?v=6771b56e"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=efea14e4"></script>
+    <script>window.MathJax = {"options": {"processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+    <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'index';</script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -132,7 +134,7 @@
 
 
 
-    <p class="title logo__title"></p>
+    <p class="title logo__title">CLASTER</p>
 
 </a></div>
         <div class="sidebar-primary-item"><ul class="navbar-icon-links navbar-nav"
@@ -174,6 +176,14 @@
         <p aria-level="2" class="caption" role="heading"><span class="caption-text">Tutorial:</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="scripts/0_Tutorial.html">TUTORIAL</a></li>
+</ul>
+<p aria-level="2" class="caption" role="heading"><span class="caption-text">Scripts:</span></p>
+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="scripts/1_Data_obtention.html">1. DATA OBTENTION &amp; PREPROCESSING</a></li>
+<li class="toctree-l1"><a class="reference internal" href="scripts/2_Run_CLASTER.html">2. CREATE &amp; RUN CLASTER</a></li>
+<li class="toctree-l1"><a class="reference internal" href="scripts/2b_Run_HyenaDNA_and_Enformer.html">2b. BENCHMARKING CLASTER WITH HYENA-DNA AND ENFORMER</a></li>
+<li class="toctree-l1"><a class="reference internal" href="scripts/3_Data_analysis.html">DATA ANALYSIS NOTEBOOK</a></li>
+
 </ul>
 
     </div>
@@ -387,6 +397,39 @@ <h1>Claster<a class="headerlink" href="#claster" title="Link to this heading">#<
 </li>
 </ul>
 </div>
+<div class="toctree-wrapper compound">
+<p aria-level="2" class="caption" role="heading"><span class="caption-text">Scripts:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="scripts/1_Data_obtention.html">1. DATA OBTENTION &amp; PREPROCESSING</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="scripts/1_Data_obtention.html#before-we-start">Before we start …</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scripts/1_Data_obtention.html#data-obtention">1. Data obtention</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scripts/1_Data_obtention.html#enhancer-perturbations">2. Enhancer perturbations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scripts/1_Data_obtention.html#benchmark-data-obtention">3. Benchmark data obtention</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="scripts/2_Run_CLASTER.html">2. CREATE &amp; RUN CLASTER</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="scripts/2_Run_CLASTER.html#create-config-files">Create config files:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scripts/2_Run_CLASTER.html#create-validation-split">Create validation split</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scripts/2_Run_CLASTER.html#training-claster"><center> Training CLASTER <center></a></li>
+<li class="toctree-l2"><a class="reference internal" href="scripts/2_Run_CLASTER.html#testing-claster"><center> Testing CLASTER <center></a></li>
+<li class="toctree-l2"><a class="reference internal" href="scripts/2_Run_CLASTER.html#predicting-in-silico-perturbed-chromatin-landscapes"><center> Predicting <em>in silico</em> perturbed chromatin landscapes <center></a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="scripts/2b_Run_HyenaDNA_and_Enformer.html">2b. BENCHMARKING CLASTER WITH HYENA-DNA AND ENFORMER</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="scripts/2b_Run_HyenaDNA_and_Enformer.html#hyena-dna">1. Hyena-DNA:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scripts/2b_Run_HyenaDNA_and_Enformer.html#enformer">2. Enformer</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="scripts/3_Data_analysis.html">DATA ANALYSIS NOTEBOOK</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="scripts/3_Data_analysis.html#packages">Packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scripts/3_Data_analysis.html#functions">Functions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scripts/3_Data_analysis.html#model-performance-on-the-baseline-prediction-task"><center> Model performance on the baseline prediction task <center></a></li>
+<li class="toctree-l2"><a class="reference internal" href="scripts/3_Data_analysis.html#in-silico-perturbations"><center> <em>In silico</em> perturbations <center></a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="scripts/3_Data_analysis.html#attributions"><center> Attributions <center></a></li>
+</ul>
+</div>
 </section>
 
 

scripts/0_Tutorial.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TUTORIAL</title>
+    <title>TUTORIAL &#8212; CLASTER</title>
 
 
 
@@ -37,13 +37,14 @@
 <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=3ee479438cf8b5e0d341" />
   <script src="../_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=3ee479438cf8b5e0d341"></script>
 
-    <script src="../_static/documentation_options.js?v=9eb32ce0"></script>
+    <script src="../_static/documentation_options.js?v=6771b56e"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/sphinx-book-theme.js?v=efea14e4"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'scripts/0_Tutorial';</script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
+    <link rel="next" title="1. DATA OBTENTION &amp; PREPROCESSING" href="1_Data_obtention.html" />
     <link rel="prev" title="Claster" href="../index.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -130,7 +131,7 @@
 
 
 
-    <p class="title logo__title"></p>
+    <p class="title logo__title">CLASTER</p>
 
 </a></div>
         <div class="sidebar-primary-item"><ul class="navbar-icon-links navbar-nav"
@@ -172,6 +173,14 @@
         <p aria-level="2" class="caption" role="heading"><span class="caption-text">Tutorial:</span></p>
 <ul class="current nav bd-sidenav">
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">TUTORIAL</a></li>
+</ul>
+<p aria-level="2" class="caption" role="heading"><span class="caption-text">Scripts:</span></p>
+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="1_Data_obtention.html">1. DATA OBTENTION &amp; PREPROCESSING</a></li>
+<li class="toctree-l1"><a class="reference internal" href="2_Run_CLASTER.html">2. CREATE &amp; RUN CLASTER</a></li>
+<li class="toctree-l1"><a class="reference internal" href="2b_Run_HyenaDNA_and_Enformer.html">2b. BENCHMARKING CLASTER WITH HYENA-DNA AND ENFORMER</a></li>
+<li class="toctree-l1"><a class="reference internal" href="3_Data_analysis.html">DATA ANALYSIS NOTEBOOK</a></li>
+
 </ul>
 
     </div>
@@ -1795,6 +1804,15 @@ <h2>3. Summary<a class="headerlink" href="#summary" title="Link to this heading"
         <p class="prev-next-title">Claster</p>
       </div>
     </a>
+    <a class="right-next"
+       href="1_Data_obtention.html"
+       title="next page">
+      <div class="prev-next-info">
+        <p class="prev-next-subtitle">next</p>
+        <p class="prev-next-title">1. DATA OBTENTION &amp; PREPROCESSING</p>
+      </div>
+      <i class="fa-solid fa-angle-right"></i>
+    </a>
 </div>
                 </footer>