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diff --git a/docs/devel/index.html b/docs/devel/index.html
diff --git a/docs/devel/pages/01_intro.html b/docs/devel/pages/01_intro.html
@@ -160,12 +160,71 @@
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
             <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true">
- <span class="menu-text">Appendices</span></a>
+ <span class="menu-text">Focus topics</span></a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true" aria-label="Toggle section">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">
+<li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/10_manipulation.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Data Manipulation</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/12_quality_control.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Exploration and Quality Control</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/11_taxonomic_information.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Taxonomic Information</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/14_alpha_diversity.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Community Diversity</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/20_beta_diversity.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Community Similarity</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/21_microbiome_community.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Community Composition</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/24_clustering.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Community Typing (Clustering)</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/30_differential_abundance.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Differential Abundance</span></span></a>
+  </div>
+</li>
+      </ul>
+</li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
+ <span class="menu-text">Appendices</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../pages/97_extra_materials.html" class="sidebar-item-text sidebar-link">

diff --git a/docs/devel/pages/04_containers.html b/docs/devel/pages/04_containers.html
@@ -79,7 +79,7 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
-<link href="../pages/97_extra_materials.html" rel="next">
+<link href="../pages/10_manipulation.html" rel="next">
 <link href="../pages/06_packages.html" rel="prev">
 <link href="../assets/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
@@ -194,12 +194,71 @@
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
             <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true">
- <span class="menu-text">Appendices</span></a>
+ <span class="menu-text">Focus topics</span></a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true" aria-label="Toggle section">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">
+<li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/10_manipulation.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Data Manipulation</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/12_quality_control.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Exploration and Quality Control</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/11_taxonomic_information.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Taxonomic Information</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/14_alpha_diversity.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Community Diversity</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/20_beta_diversity.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Community Similarity</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/21_microbiome_community.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Community Composition</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/24_clustering.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Community Typing (Clustering)</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/30_differential_abundance.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Differential Abundance</span></span></a>
+  </div>
+</li>
+      </ul>
+</li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
+ <span class="menu-text">Appendices</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../pages/97_extra_materials.html" class="sidebar-item-text sidebar-link">
@@ -1350,8 +1409,8 @@ <h1 class="title"><span id="containers" class="quarto-section-identifier"><span
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../pages/97_extra_materials.html" class="pagination-link">
-        <span class="nav-page-text"><span class="chapter-number">A</span>&nbsp; <span class="chapter-title">Extra material</span></span> <i class="bi bi-arrow-right-short"></i>
+      <a href="../pages/10_manipulation.html" class="pagination-link">
+        <span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Data Manipulation</span></span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>

diff --git a/docs/devel/pages/06_packages.html b/docs/devel/pages/06_packages.html
@@ -194,12 +194,71 @@
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
             <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true">
- <span class="menu-text">Appendices</span></a>
+ <span class="menu-text">Focus topics</span></a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true" aria-label="Toggle section">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">
+<li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/10_manipulation.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Data Manipulation</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/12_quality_control.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Exploration and Quality Control</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/11_taxonomic_information.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Taxonomic Information</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/14_alpha_diversity.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Community Diversity</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/20_beta_diversity.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Community Similarity</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/21_microbiome_community.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Community Composition</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/24_clustering.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Community Typing (Clustering)</span></span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../pages/30_differential_abundance.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Differential Abundance</span></span></a>
+  </div>
+</li>
+      </ul>
+</li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
+ <span class="menu-text">Appendices</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="../pages/97_extra_materials.html" class="sidebar-item-text sidebar-link">