Deploying to gh-pages from @ eb21768 🚀

TargetDecoy.html

@@ -467,16 +467,6 @@
     <li>
       <a href="pda_blocking_wrapup.html">2.3.2. Wrap-up DA - Blocking</a>
     </li>
-    <li>
-      <a href="technicalDetailsProteomics.html">2.3.3 Technical Details</a>
-    </li>
-    <li class="dropdown-header">---- MODULE I PROTEOMICS ----</li>
-    <li>
-      <a href="sequencing_intro.html">1.  Introduction to RNA-seq</a>
-    </li>
-    <li>
-      <a href="sequencing_countData.html">2.  Working with count data and GLMs</a>
-    </li>
   </ul>
 </li>
 <li class="dropdown">
@@ -505,16 +495,6 @@
     <li>
       <a href="pda_tutorialDesign.html">2.3. Quantification - Design</a>
     </li>
-    <li class="dropdown-header">---- MODULE II RNA-seq ----</li>
-    <li>
-      <a href="sequencingTutorial1_mapping.html">1. Read mapping</a>
-    </li>
-    <li>
-      <a href="sequencingTutorial2_DE.html">2. Working with Count Data</a>
-    </li>
-    <li>
-      <a href="scRNA-seq-Tutorial.html">3. Single Cell RNA-seq Data Analysis</a>
-    </li>
   </ul>
 </li>
       </ul>

TargetDecoyTutorial.html

@@ -458,16 +458,6 @@
     <li>
       <a href="pda_blocking_wrapup.html">2.3.2. Wrap-up DA - Blocking</a>
     </li>
-    <li>
-      <a href="technicalDetailsProteomics.html">2.3.3 Technical Details</a>
-    </li>
-    <li class="dropdown-header">---- MODULE I PROTEOMICS ----</li>
-    <li>
-      <a href="sequencing_intro.html">1.  Introduction to RNA-seq</a>
-    </li>
-    <li>
-      <a href="sequencing_countData.html">2.  Working with count data and GLMs</a>
-    </li>
   </ul>
 </li>
 <li class="dropdown">
@@ -496,16 +486,6 @@
     <li>
       <a href="pda_tutorialDesign.html">2.3. Quantification - Design</a>
     </li>
-    <li class="dropdown-header">---- MODULE II RNA-seq ----</li>
-    <li>
-      <a href="sequencingTutorial1_mapping.html">1. Read mapping</a>
-    </li>
-    <li>
-      <a href="sequencingTutorial2_DE.html">2. Working with Count Data</a>
-    </li>
-    <li>
-      <a href="scRNA-seq-Tutorial.html">3. Single Cell RNA-seq Data Analysis</a>
-    </li>
   </ul>
 </li>
       </ul>

about.html

@@ -278,16 +278,6 @@
     <li>
       <a href="pda_blocking_wrapup.html">2.3.2. Wrap-up DA - Blocking</a>
     </li>
-    <li>
-      <a href="technicalDetailsProteomics.html">2.3.3 Technical Details</a>
-    </li>
-    <li class="dropdown-header">---- MODULE I PROTEOMICS ----</li>
-    <li>
-      <a href="sequencing_intro.html">1.  Introduction to RNA-seq</a>
-    </li>
-    <li>
-      <a href="sequencing_countData.html">2.  Working with count data and GLMs</a>
-    </li>
   </ul>
 </li>
 <li class="dropdown">
@@ -316,16 +306,6 @@
     <li>
       <a href="pda_tutorialDesign.html">2.3. Quantification - Design</a>
     </li>
-    <li class="dropdown-header">---- MODULE II RNA-seq ----</li>
-    <li>
-      <a href="sequencingTutorial1_mapping.html">1. Read mapping</a>
-    </li>
-    <li>
-      <a href="sequencingTutorial2_DE.html">2. Working with Count Data</a>
-    </li>
-    <li>
-      <a href="scRNA-seq-Tutorial.html">3. Single Cell RNA-seq Data Analysis</a>
-    </li>
   </ul>
 </li>
       </ul>

cancer3x3.html

@@ -459,16 +459,6 @@
     <li>
       <a href="pda_blocking_wrapup.html">2.3.2. Wrap-up DA - Blocking</a>
     </li>
-    <li>
-      <a href="technicalDetailsProteomics.html">2.3.3 Technical Details</a>
-    </li>
-    <li class="dropdown-header">---- MODULE I PROTEOMICS ----</li>
-    <li>
-      <a href="sequencing_intro.html">1.  Introduction to RNA-seq</a>
-    </li>
-    <li>
-      <a href="sequencing_countData.html">2.  Working with count data and GLMs</a>
-    </li>
   </ul>
 </li>
 <li class="dropdown">
@@ -497,16 +487,6 @@
     <li>
       <a href="pda_tutorialDesign.html">2.3. Quantification - Design</a>
     </li>
-    <li class="dropdown-header">---- MODULE II RNA-seq ----</li>
-    <li>
-      <a href="sequencingTutorial1_mapping.html">1. Read mapping</a>
-    </li>
-    <li>
-      <a href="sequencingTutorial2_DE.html">2. Working with Count Data</a>
-    </li>
-    <li>
-      <a href="scRNA-seq-Tutorial.html">3. Single Cell RNA-seq Data Analysis</a>
-    </li>
   </ul>
 </li>
       </ul>
@@ -853,9 +833,9 @@ <h1><span class="header-section-number">5</span> Session Info</h1>
 a session info in your script so that readers of your output can see
 your particular setup of R.</p>
 <div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb36-1"><a href="#cb36-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span></code></pre></div>
-<pre><code>## R version 4.2.2 (2022-10-31)
+<pre><code>## R version 4.2.3 (2023-03-15)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Ubuntu 22.04.1 LTS
+## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
@@ -890,22 +870,22 @@ <h1><span class="header-section-number">5</span> Session Info</h1>
 ##   [4] ellipsis_0.3.2          XVector_0.36.0          fs_1.5.2               
 ##   [7] clue_0.3-61             farver_2.1.0            DT_0.23                
 ##  [10] fansi_1.0.3             lubridate_1.8.0         xml2_1.3.3             
-##  [13] codetools_0.2-18        splines_4.2.2           knitr_1.40.1           
+##  [13] codetools_0.2-18        splines_4.2.3           knitr_1.40.1           
 ##  [16] jsonlite_1.8.0          nloptr_2.0.3            broom_0.8.0            
 ##  [19] cluster_2.1.3           dbplyr_2.1.1            shinydashboard_0.7.2   
-##  [22] shiny_1.7.1             BiocManager_1.30.18     compiler_4.2.2         
+##  [22] shiny_1.7.1             BiocManager_1.30.18     compiler_4.2.3         
 ##  [25] httr_1.4.3              backports_1.4.1         assertthat_0.2.1       
 ##  [28] Matrix_1.4-1            fastmap_1.1.0           lazyeval_0.2.2         
 ##  [31] gargle_1.2.0            cli_3.3.0               later_1.3.0            
-##  [34] htmltools_0.5.2         tools_4.2.2             igraph_1.3.2           
+##  [34] htmltools_0.5.2         tools_4.2.3             igraph_1.3.2           
 ##  [37] gtable_0.3.0            glue_1.6.2              GenomeInfoDbData_1.2.8 
 ##  [40] Rcpp_1.0.8.3            cellranger_1.1.0        jquerylib_0.1.4        
 ##  [43] vctrs_0.4.1             nlme_3.1-157            rintrojs_0.3.0         
 ##  [46] xfun_0.33               lme4_1.1-29             rvest_1.0.2            
 ##  [49] mime_0.12               lifecycle_1.0.1         renv_0.15.4            
 ##  [52] googlesheets4_1.0.0     zlibbioc_1.42.0         MASS_7.3-57            
 ##  [55] scales_1.2.0            promises_1.2.0.1        hms_1.1.1              
-##  [58] ProtGenerics_1.28.0     parallel_4.2.2          AnnotationFilter_1.20.0
+##  [58] ProtGenerics_1.28.0     parallel_4.2.3          AnnotationFilter_1.20.0
 ##  [61] yaml_2.3.5              sass_0.4.1              stringi_1.7.8          
 ##  [64] highr_0.9               boot_1.3-28             BiocParallel_1.30.2    
 ##  [67] rlang_1.0.2             pkgconfig_2.0.3         bitops_1.0-7           
@@ -916,7 +896,7 @@ <h1><span class="header-section-number">5</span> Session Info</h1>
 ##  [82] haven_2.5.0             withr_2.5.0             MsCoreUtils_1.8.0      
 ##  [85] RCurl_1.98-1.6          modelr_0.1.8            crayon_1.5.1           
 ##  [88] utf8_1.2.2              tzdb_0.3.0              rmarkdown_2.14         
-##  [91] grid_4.2.2              readxl_1.4.0            data.table_1.14.2      
+##  [91] grid_4.2.3              readxl_1.4.0            data.table_1.14.2      
 ##  [94] reprex_2.0.1            digest_0.6.29           xtable_1.8-4           
 ##  [97] httpuv_1.6.5            munsell_0.5.0           viridisLite_0.4.0      
 ## [100] bslib_0.3.1             shinyjs_2.1.0</code></pre>

cancer6x6.html

@@ -459,16 +459,6 @@
     <li>
       <a href="pda_blocking_wrapup.html">2.3.2. Wrap-up DA - Blocking</a>
     </li>
-    <li>
-      <a href="technicalDetailsProteomics.html">2.3.3 Technical Details</a>
-    </li>
-    <li class="dropdown-header">---- MODULE I PROTEOMICS ----</li>
-    <li>
-      <a href="sequencing_intro.html">1.  Introduction to RNA-seq</a>
-    </li>
-    <li>
-      <a href="sequencing_countData.html">2.  Working with count data and GLMs</a>
-    </li>
   </ul>
 </li>
 <li class="dropdown">
@@ -497,16 +487,6 @@
     <li>
       <a href="pda_tutorialDesign.html">2.3. Quantification - Design</a>
     </li>
-    <li class="dropdown-header">---- MODULE II RNA-seq ----</li>
-    <li>
-      <a href="sequencingTutorial1_mapping.html">1. Read mapping</a>
-    </li>
-    <li>
-      <a href="sequencingTutorial2_DE.html">2. Working with Count Data</a>
-    </li>
-    <li>
-      <a href="scRNA-seq-Tutorial.html">3. Single Cell RNA-seq Data Analysis</a>
-    </li>
   </ul>
 </li>
       </ul>
@@ -851,9 +831,9 @@ <h1><span class="header-section-number">5</span> Session Info</h1>
 a session info in your script so that readers of your output can see
 your particular setup of R.</p>
 <div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb36-1"><a href="#cb36-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span></code></pre></div>
-<pre><code>## R version 4.2.2 (2022-10-31)
+<pre><code>## R version 4.2.3 (2023-03-15)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Ubuntu 22.04.1 LTS
+## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
@@ -888,22 +868,22 @@ <h1><span class="header-section-number">5</span> Session Info</h1>
 ##   [4] ellipsis_0.3.2          XVector_0.36.0          fs_1.5.2               
 ##   [7] clue_0.3-61             farver_2.1.0            DT_0.23                
 ##  [10] fansi_1.0.3             lubridate_1.8.0         xml2_1.3.3             
-##  [13] codetools_0.2-18        splines_4.2.2           knitr_1.40.1           
+##  [13] codetools_0.2-18        splines_4.2.3           knitr_1.40.1           
 ##  [16] jsonlite_1.8.0          nloptr_2.0.3            broom_0.8.0            
 ##  [19] cluster_2.1.3           dbplyr_2.1.1            shinydashboard_0.7.2   
-##  [22] shiny_1.7.1             BiocManager_1.30.18     compiler_4.2.2         
+##  [22] shiny_1.7.1             BiocManager_1.30.18     compiler_4.2.3         
 ##  [25] httr_1.4.3              backports_1.4.1         assertthat_0.2.1       
 ##  [28] Matrix_1.4-1            fastmap_1.1.0           lazyeval_0.2.2         
 ##  [31] gargle_1.2.0            cli_3.3.0               later_1.3.0            
-##  [34] htmltools_0.5.2         tools_4.2.2             igraph_1.3.2           
+##  [34] htmltools_0.5.2         tools_4.2.3             igraph_1.3.2           
 ##  [37] gtable_0.3.0            glue_1.6.2              GenomeInfoDbData_1.2.8 
 ##  [40] Rcpp_1.0.8.3            cellranger_1.1.0        jquerylib_0.1.4        
 ##  [43] vctrs_0.4.1             nlme_3.1-157            rintrojs_0.3.0         
 ##  [46] xfun_0.33               lme4_1.1-29             rvest_1.0.2            
 ##  [49] mime_0.12               lifecycle_1.0.1         renv_0.15.4            
 ##  [52] googlesheets4_1.0.0     zlibbioc_1.42.0         MASS_7.3-57            
 ##  [55] scales_1.2.0            promises_1.2.0.1        hms_1.1.1              
-##  [58] ProtGenerics_1.28.0     parallel_4.2.2          AnnotationFilter_1.20.0
+##  [58] ProtGenerics_1.28.0     parallel_4.2.3          AnnotationFilter_1.20.0
 ##  [61] yaml_2.3.5              sass_0.4.1              stringi_1.7.8          
 ##  [64] highr_0.9               boot_1.3-28             BiocParallel_1.30.2    
 ##  [67] rlang_1.0.2             pkgconfig_2.0.3         bitops_1.0-7           
@@ -914,7 +894,7 @@ <h1><span class="header-section-number">5</span> Session Info</h1>
 ##  [82] haven_2.5.0             withr_2.5.0             MsCoreUtils_1.8.0      
 ##  [85] RCurl_1.98-1.6          modelr_0.1.8            crayon_1.5.1           
 ##  [88] utf8_1.2.2              tzdb_0.3.0              rmarkdown_2.14         
-##  [91] grid_4.2.2              readxl_1.4.0            data.table_1.14.2      
+##  [91] grid_4.2.3              readxl_1.4.0            data.table_1.14.2      
 ##  [94] reprex_2.0.1            digest_0.6.29           xtable_1.8-4           
 ##  [97] httpuv_1.6.5            munsell_0.5.0           viridisLite_0.4.0      
 ## [100] bslib_0.3.1             shinyjs_2.1.0</code></pre>

cptac_maxLFQ.html

@@ -459,16 +459,6 @@
     <li>
       <a href="pda_blocking_wrapup.html">2.3.2. Wrap-up DA - Blocking</a>
     </li>
-    <li>
-      <a href="technicalDetailsProteomics.html">2.3.3 Technical Details</a>
-    </li>
-    <li class="dropdown-header">---- MODULE I PROTEOMICS ----</li>
-    <li>
-      <a href="sequencing_intro.html">1.  Introduction to RNA-seq</a>
-    </li>
-    <li>
-      <a href="sequencing_countData.html">2.  Working with count data and GLMs</a>
-    </li>
   </ul>
 </li>
 <li class="dropdown">
@@ -497,16 +487,6 @@
     <li>
       <a href="pda_tutorialDesign.html">2.3. Quantification - Design</a>
     </li>
-    <li class="dropdown-header">---- MODULE II RNA-seq ----</li>
-    <li>
-      <a href="sequencingTutorial1_mapping.html">1. Read mapping</a>
-    </li>
-    <li>
-      <a href="sequencingTutorial2_DE.html">2. Working with Count Data</a>
-    </li>
-    <li>
-      <a href="scRNA-seq-Tutorial.html">3. Single Cell RNA-seq Data Analysis</a>
-    </li>
   </ul>
 </li>
       </ul>
@@ -816,9 +796,9 @@ <h1><span class="header-section-number">6</span> Session Info</h1>
 a session info in your script so that readers of your output can see
 your particular setup of R.</p>
 <div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb28-1"><a href="#cb28-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span></code></pre></div>
-<pre><code>## R version 4.2.2 (2022-10-31)
+<pre><code>## R version 4.2.3 (2023-03-15)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Ubuntu 22.04.1 LTS
+## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
@@ -853,22 +833,22 @@ <h1><span class="header-section-number">6</span> Session Info</h1>
 ##   [4] ellipsis_0.3.2          XVector_0.36.0          fs_1.5.2               
 ##   [7] clue_0.3-61             farver_2.1.0            DT_0.23                
 ##  [10] fansi_1.0.3             lubridate_1.8.0         xml2_1.3.3             
-##  [13] codetools_0.2-18        splines_4.2.2           knitr_1.40.1           
+##  [13] codetools_0.2-18        splines_4.2.3           knitr_1.40.1           
 ##  [16] jsonlite_1.8.0          nloptr_2.0.3            broom_0.8.0            
 ##  [19] cluster_2.1.3           dbplyr_2.1.1            shinydashboard_0.7.2   
-##  [22] shiny_1.7.1             BiocManager_1.30.18     compiler_4.2.2         
+##  [22] shiny_1.7.1             BiocManager_1.30.18     compiler_4.2.3         
 ##  [25] httr_1.4.3              backports_1.4.1         assertthat_0.2.1       
 ##  [28] Matrix_1.4-1            fastmap_1.1.0           lazyeval_0.2.2         
 ##  [31] gargle_1.2.0            cli_3.3.0               later_1.3.0            
-##  [34] htmltools_0.5.2         tools_4.2.2             igraph_1.3.2           
+##  [34] htmltools_0.5.2         tools_4.2.3             igraph_1.3.2           
 ##  [37] gtable_0.3.0            glue_1.6.2              GenomeInfoDbData_1.2.8 
 ##  [40] Rcpp_1.0.8.3            cellranger_1.1.0        jquerylib_0.1.4        
 ##  [43] vctrs_0.4.1             nlme_3.1-157            rintrojs_0.3.0         
 ##  [46] xfun_0.33               lme4_1.1-29             rvest_1.0.2            
 ##  [49] mime_0.12               lifecycle_1.0.1         renv_0.15.4            
 ##  [52] googlesheets4_1.0.0     zlibbioc_1.42.0         MASS_7.3-57            
 ##  [55] scales_1.2.0            promises_1.2.0.1        hms_1.1.1              
-##  [58] ProtGenerics_1.28.0     parallel_4.2.2          AnnotationFilter_1.20.0
+##  [58] ProtGenerics_1.28.0     parallel_4.2.3          AnnotationFilter_1.20.0
 ##  [61] yaml_2.3.5              sass_0.4.1              stringi_1.7.8          
 ##  [64] highr_0.9               boot_1.3-28             BiocParallel_1.30.2    
 ##  [67] rlang_1.0.2             pkgconfig_2.0.3         bitops_1.0-7           
@@ -879,7 +859,7 @@ <h1><span class="header-section-number">6</span> Session Info</h1>
 ##  [82] haven_2.5.0             withr_2.5.0             MsCoreUtils_1.8.0      
 ##  [85] RCurl_1.98-1.6          modelr_0.1.8            crayon_1.5.1           
 ##  [88] utf8_1.2.2              tzdb_0.3.0              rmarkdown_2.14         
-##  [91] grid_4.2.2              readxl_1.4.0            data.table_1.14.2      
+##  [91] grid_4.2.3              readxl_1.4.0            data.table_1.14.2      
 ##  [94] reprex_2.0.1            digest_0.6.29           xtable_1.8-4           
 ##  [97] httpuv_1.6.5            munsell_0.5.0           viridisLite_0.4.0      
 ## [100] bslib_0.3.1             shinyjs_2.1.0</code></pre>