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diff --git a/CorticalCells_GSM2861511_E135-analysis.html b/CorticalCells_GSM2861511_E135-analysis.html
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diff --git a/CorticalCells_GSM2861514_E175-analysis.html b/CorticalCells_GSM2861514_E175-analysis.html
@@ -410,7 +410,7 @@
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-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
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diff --git a/DEA_Seurat_COTAN.html b/DEA_Seurat_COTAN.html
@@ -412,7 +412,7 @@
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diff --git a/DEA_Type1Er.html b/DEA_Type1Er.html
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diff --git a/FDR_DataSetCreation_ByClusterMerging.html b/FDR_DataSetCreation_ByClusterMerging.html
@@ -414,7 +414,7 @@
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diff --git a/FDR_analisys.html b/FDR_analisys.html
@@ -109,7 +109,7 @@
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-      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./DEA_Type1Error.html">DEA evaluation</a></li><li class="breadcrumb-item"><a href="./FDR_analisys.html">FDR analysis - define DE genes</a></li></ol></nav>
+      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./DEA_Type1Er.html">DEA evaluation</a></li><li class="breadcrumb-item"><a href="./FDR_analisys.html">FDR analysis - define DE genes</a></li></ol></nav>
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-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
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diff --git a/FDR_analisysResults3_10.html b/FDR_analisysResults3_10.html
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diff --git a/FDR_analisysResults5.html b/FDR_analisysResults5.html
@@ -109,7 +109,7 @@
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-      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./DEA_Type1Error.html">DEA evaluation</a></li><li class="breadcrumb-item"><a href="./FDR_analisysResults3_10.html">FDR and TPR - ROC curves</a></li><li class="breadcrumb-item"><a href="./FDR_analisysResults5.html">Results - thresholds true 5%</a></li></ol></nav>
+      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./DEA_Type1Er.html">DEA evaluation</a></li><li class="breadcrumb-item"><a href="./FDR_analisysResults3_10.html">FDR and TPR - ROC curves</a></li><li class="breadcrumb-item"><a href="./FDR_analisysResults5.html">Results - thresholds true 5%</a></li></ol></nav>
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@@ -412,7 +412,7 @@
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-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
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diff --git a/FDR_analisysResults5_20.html b/FDR_analisysResults5_20.html
@@ -109,7 +109,7 @@
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         <i class="bi bi-layout-text-sidebar-reverse"></i>
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-      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./DEA_Type1Error.html">DEA evaluation</a></li><li class="breadcrumb-item"><a href="./FDR_analisysResults3_10.html">FDR and TPR - ROC curves</a></li><li class="breadcrumb-item"><a href="./FDR_analisysResults5_20.html">Results - thresholds true 5% 20%</a></li></ol></nav>
+      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./DEA_Type1Er.html">DEA evaluation</a></li><li class="breadcrumb-item"><a href="./FDR_analisysResults3_10.html">FDR and TPR - ROC curves</a></li><li class="breadcrumb-item"><a href="./FDR_analisysResults5_20.html">Results - thresholds true 5% 20%</a></li></ol></nav>
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@@ -412,7 +412,7 @@
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-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
+  <a href="./DEA_Type1Er.html" class="sidebar-item-text sidebar-link">
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 </li>

diff --git a/FDR_analysisResultsLFC.html b/FDR_analysisResultsLFC.html
@@ -108,7 +108,7 @@
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         <i class="bi bi-layout-text-sidebar-reverse"></i>
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-      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./DEA_Type1Error.html">DEA evaluation</a></li><li class="breadcrumb-item"><a href="./FDR_analisysResults3_10.html">FDR and TPR - ROC curves</a></li><li class="breadcrumb-item"><a href="./FDR_analysisResultsLFC.html">Results - Log Fold Change</a></li></ol></nav>
+      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./DEA_Type1Er.html">DEA evaluation</a></li><li class="breadcrumb-item"><a href="./FDR_analisysResults3_10.html">FDR and TPR - ROC curves</a></li><li class="breadcrumb-item"><a href="./FDR_analysisResultsLFC.html">Results - Log Fold Change</a></li></ol></nav>
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-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
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diff --git a/FindUniformOrigCluster.html b/FindUniformOrigCluster.html
@@ -410,7 +410,7 @@
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diff --git a/ForebrainDorsal_E135-analysis.html b/ForebrainDorsal_E135-analysis.html
@@ -410,7 +410,7 @@
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diff --git a/ForebrainDorsal_E150-analysis.html b/ForebrainDorsal_E150-analysis.html
@@ -410,7 +410,7 @@
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+  <a href="./DEA_Type1Er.html" class="sidebar-item-text sidebar-link">
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diff --git a/ForebrainDorsal_E175-analysis.html b/ForebrainDorsal_E175-analysis.html
@@ -410,7 +410,7 @@
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           <li class="sidebar-item">
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+  <a href="./DEA_Type1Er.html" class="sidebar-item-text sidebar-link">
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diff --git a/ForebrainDorsal_MixingUniformClusters_ToEstimateGDISensitivity.html b/ForebrainDorsal_MixingUniformClusters_ToEstimateGDISensitivity.html
@@ -414,7 +414,7 @@
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           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
+  <a href="./DEA_Type1Er.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Type I error</span></a>
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diff --git a/ForebrainLaManno2021ClustersGDI.html b/ForebrainLaManno2021ClustersGDI.html
@@ -412,7 +412,7 @@
       <ul id="quarto-sidebar-section-10" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
+  <a href="./DEA_Type1Er.html" class="sidebar-item-text sidebar-link">
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diff --git a/GDI_Increment_From_Mixing.html b/GDI_Increment_From_Mixing.html
@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 <meta name="author" content="Marco Fantozzi">
-<meta name="dcterms.date" content="2024-05-30">
+<meta name="dcterms.date" content="2024-06-03">
 
 <title>COTAN Datasets analysis - GDI Increment From Mixing</title>
 <style>
@@ -412,7 +412,7 @@
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           <li class="sidebar-item">
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-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
+  <a href="./DEA_Type1Er.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Type I error</span></a>
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 </li>
@@ -529,7 +529,7 @@ <h1 class="title">GDI Increment From Mixing</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">May 30, 2024</p>
+      <p class="date">June 3, 2024</p>
     </div>
   </div>
 
@@ -763,7 +763,7 @@ <h2 class="anchored" data-anchor-id="merge-all-data-and-plot-it-using-the-distan
 <div class="cell-output-display">
 <p><img src="GDI_Increment_From_Mixing_files/figure-html/unnamed-chunk-10-1.png" class="img-fluid" width="672"></p>
 </div>
-<div class="sourceCode cell-code" id="cb16"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a><span class="fu">pdf</span>(<span class="st">"Results/GDI_Sensitivity/GDI_increment.pdf"</span>,<span class="at">width =</span> <span class="dv">7</span>, <span class="at">height =</span> <span class="dv">10</span>)</span>
+<div class="sourceCode cell-code" id="cb16"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a><span class="fu">pdf</span>(<span class="st">"Results/GDI_Sensitivity/GDI_increment.pdf"</span>,<span class="at">width =</span> <span class="dv">7</span>, <span class="at">height =</span> <span class="dv">7</span>)</span>
 <span id="cb16-2"><a href="#cb16-2" aria-hidden="true" tabindex="-1"></a><span class="fu">plot</span>(final.plot1)</span>
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 <div class="cell-output cell-output-stdout">
@@ -808,7 +808,7 @@ <h2 class="anchored" data-anchor-id="merge-all-data-and-plot-it-using-the-distan
 <div class="cell-output-display">
 <p><img src="GDI_Increment_From_Mixing_files/figure-html/unnamed-chunk-10-3.png" class="img-fluid" width="672"></p>
 </div>
-<div class="sourceCode cell-code" id="cb20"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="fu">pdf</span>(<span class="st">"Results/GDI_Sensitivity/GDI_TopPercentile.pdf"</span>,<span class="at">width =</span> <span class="dv">7</span>, <span class="at">height =</span> <span class="dv">10</span>)</span>
+<div class="sourceCode cell-code" id="cb20"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="fu">pdf</span>(<span class="st">"Results/GDI_Sensitivity/GDI_TopPercentile.pdf"</span>,<span class="at">width =</span> <span class="dv">7</span>, <span class="at">height =</span> <span class="dv">7</span> )</span>
 <span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a><span class="fu">plot</span>(final.plot2)</span>
 <span id="cb20-3"><a href="#cb20-3" aria-hidden="true" tabindex="-1"></a><span class="fu">dev.off</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
@@ -879,13 +879,13 @@ <h2 class="anchored" data-anchor-id="compare-estimated-vs-real-gdi-increment">Co
  [5] hms_1.1.3          digest_0.6.35      magrittr_2.0.3     evaluate_0.23     
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-[17] cli_3.6.2          splines_4.4.0      munsell_0.5.1      withr_3.0.0       
+[17] cli_3.6.2          munsell_0.5.1      splines_4.4.0      withr_3.0.0       
 [21] yaml_2.3.8         tools_4.4.0        tzdb_0.4.0         colorspace_2.1-0  
 [25] vctrs_0.6.5        R6_2.5.1           lifecycle_1.0.4    htmlwidgets_1.6.4 
 [29] pkgconfig_2.0.3    RcppParallel_5.1.7 pillar_1.9.0       gtable_0.3.5      
 [33] glue_1.7.0         Rcpp_1.0.12        xfun_0.44          tidyselect_1.2.1  
-[37] rstudioapi_0.16.0  knitr_1.46         farver_2.1.2       nlme_3.1-164      
-[41] htmltools_0.5.8.1  labeling_0.4.3     rmarkdown_2.27     compiler_4.4.0    </code></pre>
+[37] knitr_1.46         farver_2.1.2       nlme_3.1-164       htmltools_0.5.8.1 
+[41] labeling_0.4.3     rmarkdown_2.27     compiler_4.4.0    </code></pre>
 </div>
 </div>
 

diff --git a/GDI_Increment_From_Mixing_files/figure-html/unnamed-chunk-10-1.png b/GDI_Increment_From_Mixing_files/figure-html/unnamed-chunk-10-1.png
diff --git a/GDI_Increment_From_Mixing_files/figure-html/unnamed-chunk-10-2.png b/GDI_Increment_From_Mixing_files/figure-html/unnamed-chunk-10-2.png
diff --git a/GDI_Increment_From_Mixing_files/figure-html/unnamed-chunk-10-3.png b/GDI_Increment_From_Mixing_files/figure-html/unnamed-chunk-10-3.png
diff --git a/GDI_Increment_From_Mixing_files/figure-html/unnamed-chunk-10-4.png b/GDI_Increment_From_Mixing_files/figure-html/unnamed-chunk-10-4.png
diff --git a/GDI_vairance.html b/GDI_vairance.html
@@ -413,7 +413,7 @@
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           <li class="sidebar-item">
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-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
+  <a href="./DEA_Type1Er.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Type I error</span></a>
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 </li>

diff --git a/Mouse_Cortex_E14.5.html b/Mouse_Cortex_E14.5.html
@@ -410,7 +410,7 @@
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           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
+  <a href="./DEA_Type1Er.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Type I error</span></a>
   </div>
 </li>

diff --git a/NonCT_clusters.html b/NonCT_clusters.html
@@ -412,7 +412,7 @@
       <ul id="quarto-sidebar-section-10" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
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-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
+  <a href="./DEA_Type1Er.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Type I error</span></a>
   </div>
 </li>

diff --git a/OriginalClustersDistanceEvaluation.html b/OriginalClustersDistanceEvaluation.html
@@ -414,7 +414,7 @@
       <ul id="quarto-sidebar-section-10" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
+  <a href="./DEA_Type1Er.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Type I error</span></a>
   </div>
 </li>

diff --git a/PBMC1_filtering.html b/PBMC1_filtering.html
@@ -411,7 +411,7 @@
       <ul id="quarto-sidebar-section-10" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
+  <a href="./DEA_Type1Er.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Type I error</span></a>
   </div>
 </li>

diff --git a/PBMC2_filtering.html b/PBMC2_filtering.html
@@ -411,7 +411,7 @@
       <ul id="quarto-sidebar-section-10" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
+  <a href="./DEA_Type1Er.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Type I error</span></a>
   </div>
 </li>

diff --git a/PBMC3_filtering.html b/PBMC3_filtering.html
@@ -411,7 +411,7 @@
       <ul id="quarto-sidebar-section-10" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./DEA_Type1Error.html" class="sidebar-item-text sidebar-link">
+  <a href="./DEA_Type1Er.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Type I error</span></a>
   </div>
 </li>