deploy: bb270c7

_sources/scripts/2_Run_CLASTER.ipynb

@@ -5617,7 +5617,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## <center> Training CLASTER <center>\n",
+    "## Training CLASTER\n",
     "The model can be trained by running the following command:\n",
     "\n",
     "```bash\n",
@@ -5689,7 +5689,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## <center> Testing CLASTER <center>\n",
+    "## Testing CLASTER\n",
     "\n",
     "> _Note:_ \n",
     ">\n",
@@ -5776,7 +5776,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## <center> Predicting _in silico_ perturbed chromatin landscapes <center>\n",
+    "## Predicting _in silico_ perturbed chromatin landscapes\n",
     "\n",
     ">Note: Make sure to create the output folder beforehand: ./runs/perturbation_runs/gene_expression_only_chrom_pure_conv/"
    ]

_sources/scripts/3_Data_analysis.ipynb

@@ -958,7 +958,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## <center> Model performance on the baseline prediction task <center>\n",
+    "## Model performance on the baseline prediction task\n",
     "**Figure 1 and related supplementary figures**\n",
     "\n",
     "> Note: ⏰ This took 42 min when analysing all genes and enhancers in chr4:\n",
@@ -1256,7 +1256,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## <center> _In silico_ perturbations <center>\n",
+    "## _In silico_ perturbations\n",
     "\n",
     "**Figure 2 and related supplementary figures**\n",
     "\n"
@@ -1962,7 +1962,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# <center> Attributions <center>\n",
+    "# Attributions\n",
     "\n",
     "Now we will compute the attribution scores for every input position (4,10.001) towards every output (401). This mechanism tells how important is every input position (i.e. a given bin in each input track in the landscape or a given bin in a Micro-C matrix) for the prediction of the EU-seq levels at the position described by a given target node (401 targets). It also tells us the direction of the association.\n",
     "The original paper can be found at:\n",

index.html

@@ -410,9 +410,9 @@ <h1>Claster<a class="headerlink" href="#claster" title="Link to this heading">#<
 <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>
+<li class="toctree-l2"><a class="reference internal" href="scripts/2_Run_CLASTER.html#training-claster">Training CLASTER</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scripts/2_Run_CLASTER.html#testing-claster">Testing CLASTER</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scripts/2_Run_CLASTER.html#predicting-in-silico-perturbed-chromatin-landscapes">Predicting <em>in silico</em> perturbed chromatin landscapes</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>
@@ -423,11 +423,11 @@ <h1>Claster<a class="headerlink" href="#claster" title="Link to this heading">#<
 <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>
+<li class="toctree-l2"><a class="reference internal" href="scripts/3_Data_analysis.html#model-performance-on-the-baseline-prediction-task">Model performance on the baseline prediction task</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scripts/3_Data_analysis.html#in-silico-perturbations"><em>In silico</em> perturbations</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="scripts/3_Data_analysis.html#attributions"><center> Attributions <center></a></li>
+<li class="toctree-l1"><a class="reference internal" href="scripts/3_Data_analysis.html#attributions">Attributions</a></li>
 </ul>
 </div>
 </section>

scripts/2_Run_CLASTER.html

@@ -409,9 +409,9 @@ <h2> Contents </h2>
                 <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#create-config-files">Create config files:</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#create-validation-split">Create validation split</a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#training-claster"><center> Training CLASTER <center></center></center></a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#testing-claster"><center> Testing CLASTER <center></center></center></a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#predicting-in-silico-perturbed-chromatin-landscapes"><center> Predicting <em>in silico</em> perturbed chromatin landscapes <center></center></center></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#training-claster">Training CLASTER</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#testing-claster">Testing CLASTER</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#predicting-in-silico-perturbed-chromatin-landscapes">Predicting <em>in silico</em> perturbed chromatin landscapes</a></li>
 </ul>
             </nav>
         </div>
@@ -6000,7 +6000,7 @@ <h2>Create validation split<a class="headerlink" href="#create-validation-split"
 ENSMUSG00000055660.9_rev</p>
 </section>
 <section id="training-claster">
-<h2><center> Training CLASTER <center><a class="headerlink" href="#training-claster" title="Link to this heading">#</a></h2>
+<h2>Training CLASTER<a class="headerlink" href="#training-claster" title="Link to this heading">#</a></h2>
 <p>The model can be trained by running the following command:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>eirtrain<span class="w"> </span><span class="se">\</span>
 --global_configs<span class="w"> </span>./configurations/conf_pure_conv/globals.yaml<span class="w"> </span><span class="se">\</span>
@@ -6063,7 +6063,7 @@ <h2><center> Training CLASTER <center><a class="headerlink" href="#training-clas
 </div>
 </section>
 <section id="testing-claster">
-<h2><center> Testing CLASTER <center><a class="headerlink" href="#testing-claster" title="Link to this heading">#</a></h2>
+<h2>Testing CLASTER<a class="headerlink" href="#testing-claster" title="Link to this heading">#</a></h2>
 <blockquote>
 <div><p><em>Note:</em></p>
 <ol class="arabic simple">
@@ -6132,7 +6132,7 @@ <h2><center> Testing CLASTER <center><a class="headerlink" href="#testing-claste
 </div>
 </section>
 <section id="predicting-in-silico-perturbed-chromatin-landscapes">
-<h2><center> Predicting <em>in silico</em> perturbed chromatin landscapes <center><a class="headerlink" href="#predicting-in-silico-perturbed-chromatin-landscapes" title="Link to this heading">#</a></h2>
+<h2>Predicting <em>in silico</em> perturbed chromatin landscapes<a class="headerlink" href="#predicting-in-silico-perturbed-chromatin-landscapes" title="Link to this heading">#</a></h2>
 <blockquote>
 <div><p>Note: Make sure to create the output folder beforehand: ./runs/perturbation_runs/gene_expression_only_chrom_pure_conv/</p>
 </div></blockquote>
@@ -6208,9 +6208,9 @@ <h2><center> Predicting <em>in silico</em> perturbed chromatin landscapes <cente
     <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#create-config-files">Create config files:</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#create-validation-split">Create validation split</a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#training-claster"><center> Training CLASTER <center></center></center></a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#testing-claster"><center> Testing CLASTER <center></center></center></a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#predicting-in-silico-perturbed-chromatin-landscapes"><center> Predicting <em>in silico</em> perturbed chromatin landscapes <center></center></center></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#training-claster">Training CLASTER</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#testing-claster">Testing CLASTER</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#predicting-in-silico-perturbed-chromatin-landscapes">Predicting <em>in silico</em> perturbed chromatin landscapes</a></li>
 </ul>
   </nav></div>
 

scripts/3_Data_analysis.html

@@ -409,11 +409,11 @@ <h2> Contents </h2>
 <li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#">DATA ANALYSIS NOTEBOOK</a><ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#packages">Packages</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#functions">Functions</a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#model-performance-on-the-baseline-prediction-task"><center> Model performance on the baseline prediction task <center></center></center></a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#in-silico-perturbations"><center> <em>In silico</em> perturbations <center></center></center></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#model-performance-on-the-baseline-prediction-task">Model performance on the baseline prediction task</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#in-silico-perturbations"><em>In silico</em> perturbations</a></li>
 </ul>
 </li>
-<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#attributions"><center> Attributions <center></center></center></a></li>
+<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#attributions">Attributions</a></li>
 </ul>
 
             </nav>
@@ -1369,7 +1369,7 @@ <h2>Functions<a class="headerlink" href="#functions" title="Link to this heading
 </div>
 </section>
 <section id="model-performance-on-the-baseline-prediction-task">
-<h2><center> Model performance on the baseline prediction task <center><a class="headerlink" href="#model-performance-on-the-baseline-prediction-task" title="Link to this heading">#</a></h2>
+<h2>Model performance on the baseline prediction task<a class="headerlink" href="#model-performance-on-the-baseline-prediction-task" title="Link to this heading">#</a></h2>
 <p><strong>Figure 1 and related supplementary figures</strong></p>
 <blockquote>
 <div><p>Note: ⏰ This took 42 min when analysing all genes and enhancers in chr4:</p>
@@ -1611,7 +1611,7 @@ <h2><center> Model performance on the baseline prediction task <center><a class=
 </div>
 </section>
 <section id="in-silico-perturbations">
-<h2><center> <em>In silico</em> perturbations <center><a class="headerlink" href="#in-silico-perturbations" title="Link to this heading">#</a></h2>
+<h2><em>In silico</em> perturbations<a class="headerlink" href="#in-silico-perturbations" title="Link to this heading">#</a></h2>
 <p><strong>Figure 2 and related supplementary figures</strong></p>
 <blockquote>
 <div><p>⏰ The following step takes a few minutes</p>
@@ -2156,7 +2156,7 @@ <h2><center> <em>In silico</em> perturbations <center><a class="headerlink" href
 </section>
 </section>
 <section class="tex2jax_ignore mathjax_ignore" id="attributions">
-<h1><center> Attributions <center><a class="headerlink" href="#attributions" title="Link to this heading">#</a></h1>
+<h1>Attributions<a class="headerlink" href="#attributions" title="Link to this heading">#</a></h1>
 <p>Now we will compute the attribution scores for every input position (4,10.001) towards every output (401). This mechanism tells how important is every input position (i.e. a given bin in each input track in the landscape or a given bin in a Micro-C matrix) for the prediction of the EU-seq levels at the position described by a given target node (401 targets). It also tells us the direction of the association.
 The original paper can be found at:</p>
 <p>https://arxiv.org/abs/1703.01365</p>
@@ -2721,11 +2721,11 @@ <h1><center> Attributions <center><a class="headerlink" href="#attributions" tit
 <li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#">DATA ANALYSIS NOTEBOOK</a><ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#packages">Packages</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#functions">Functions</a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#model-performance-on-the-baseline-prediction-task"><center> Model performance on the baseline prediction task <center></center></center></a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#in-silico-perturbations"><center> <em>In silico</em> perturbations <center></center></center></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#model-performance-on-the-baseline-prediction-task">Model performance on the baseline prediction task</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#in-silico-perturbations"><em>In silico</em> perturbations</a></li>
 </ul>
 </li>
-<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#attributions"><center> Attributions <center></center></center></a></li>
+<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#attributions">Attributions</a></li>
 </ul>
 
   </nav></div>