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seriph78 · Jun 4, 2024 · c58e4dd · c58e4dd
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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-606a4b79
+bef7808e
diff --git a/CorticalCells_GSM2861511_E135-analysis.html b/CorticalCells_GSM2861511_E135-analysis.html
@@ -483,6 +483,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/CorticalCells_GSM2861514_E175-analysis.html b/CorticalCells_GSM2861514_E175-analysis.html
@@ -483,6 +483,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/DEA_Seurat_COTAN.html b/DEA_Seurat_COTAN.html
@@ -485,6 +485,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/DEA_Type1Er.html b/DEA_Type1Er.html
@@ -485,6 +485,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/FDR_DataSetCreation_ByClusterMerging.html b/FDR_DataSetCreation_ByClusterMerging.html
@@ -487,6 +487,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/FDR_analisys.html b/FDR_analisys.html
@@ -485,6 +485,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/FDR_analisysResults3_10.html b/FDR_analisysResults3_10.html
@@ -485,6 +485,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/FDR_analisysResults5.html b/FDR_analisysResults5.html
@@ -485,6 +485,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/FDR_analisysResults5_20.html b/FDR_analisysResults5_20.html
@@ -485,6 +485,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/FDR_analysisResultsLFC.html b/FDR_analysisResultsLFC.html
@@ -484,6 +484,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/FindUniformOrigCluster.html b/FindUniformOrigCluster.html
@@ -483,6 +483,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/ForebrainDorsal_E135-analysis.html b/ForebrainDorsal_E135-analysis.html
@@ -483,6 +483,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/ForebrainDorsal_E150-analysis.html b/ForebrainDorsal_E150-analysis.html
@@ -483,6 +483,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/ForebrainDorsal_E175-analysis.html b/ForebrainDorsal_E175-analysis.html
@@ -483,6 +483,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/ForebrainDorsal_MixingUniformClusters_ToEstimateGDISensitivity.html b/ForebrainDorsal_MixingUniformClusters_ToEstimateGDISensitivity.html
@@ -487,6 +487,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/ForebrainLaManno2021ClustersGDI.html b/ForebrainLaManno2021ClustersGDI.html
@@ -485,6 +485,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/GDI_Increment_From_Mixing.html b/GDI_Increment_From_Mixing.html
@@ -485,6 +485,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/GDI_vairance.html b/GDI_vairance.html
@@ -486,6 +486,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/Mouse_Cortex_E14.5.html b/Mouse_Cortex_E14.5.html
@@ -483,6 +483,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/NonCT_clusters.html b/NonCT_clusters.html
@@ -485,6 +485,18 @@
   <a href="./src/scanpyFDR.py" class="sidebar-item-text sidebar-link">
  <span class="menu-text">ScamPy FDR code</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scanpy.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of scanpy clustering and DEA</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./scvi-tools.ipynb" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Example of ScVI clustering and DEA</span></a>
+  </div>
 </li>
       </ul>
   </li>