correct section in advance R

UCL-BLIC · Jan 26, 2024 · acf81ae · acf81ae
1 parent 32a31bc
commit acf81ae
Show file tree

Hide file tree

Showing 21 changed files with 2,380 additions and 1,653 deletions.
diff --git a/docs/Fundamentals/Advanced-R.css b/docs/Fundamentals/Advanced-R.css
@@ -123,16 +123,16 @@
     width: 340px;
   }
 }.u-section-4 .u-sheet-1 {
-  min-height: 885px;
+  min-height: 883px;
 }
 
 .u-section-4 .u-layout-wrap-1 {
   margin-top: 37px;
-  margin-bottom: 20px;
+  margin-bottom: 37px;
 }
 
 .u-section-4 .u-layout-cell-1 {
-  min-height: 326px;
+  min-height: 354px;
 }
 
 .u-section-4 .u-container-layout-1 {
@@ -157,7 +157,7 @@
 }
 
 .u-section-4 .u-layout-cell-2 {
-  min-height: 326px;
+  min-height: 354px;
 }
 
 .u-section-4 .u-container-layout-2 {
@@ -187,7 +187,7 @@
 }
 
 .u-section-4 .u-layout-cell-3 {
-  min-height: 320px;
+  min-height: 290px;
 }
 
 .u-section-4 .u-container-layout-3 {
@@ -212,7 +212,7 @@
 }
 
 .u-section-4 .u-layout-cell-4 {
-  min-height: 320px;
+  min-height: 290px;
 }
 
 .u-section-4 .u-container-layout-4 {
@@ -250,11 +250,11 @@
 }
 
 .u-section-4 .u-layout-cell-5 {
-  min-height: 185px;
+  min-height: 175px;
 }
 
 .u-section-4 .u-container-layout-5 {
-  padding: 34px 30px;
+  padding: 17px 30px;
 }
 
 .u-section-4 .u-text-5 {
@@ -279,7 +279,7 @@
 
   .u-section-4 .u-layout-cell-1 {
     background-position: 50% 50%;
-    min-height: 269px;
+    min-height: 292px;
   }
 
   .u-section-4 .u-text-1 {
@@ -292,19 +292,19 @@
   }
 
   .u-section-4 .u-layout-cell-2 {
-    min-height: 269px;
+    min-height: 292px;
   }
 
   .u-section-4 .u-text-2 {
     margin-top: -1px;
   }
 
   .u-section-4 .u-layout-cell-3 {
-    min-height: 264px;
+    min-height: 239px;
   }
 
   .u-section-4 .u-layout-cell-4 {
-    min-height: 264px;
+    min-height: 239px;
   }
 
   .u-section-4 .u-text-4 {
@@ -313,7 +313,7 @@
   }
 
   .u-section-4 .u-layout-cell-5 {
-    min-height: 153px;
+    min-height: 145px;
   }
 
   .u-section-4 .u-text-5 {
@@ -341,11 +341,6 @@
   .u-section-4 .u-layout-cell-5 {
     min-height: 100px;
   }
-
-  .u-section-4 .u-container-layout-5 {
-    padding-top: 30px;
-    padding-bottom: 30px;
-  }
 }
 
 @media (max-width: 767px) {

diff --git a/docs/Fundamentals/Advanced-R.html b/docs/Fundamentals/Advanced-R.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="Advanced-R.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 
@@ -128,7 +128,7 @@ <h1 class="u-align-center u-text u-text-default u-text-1">TO DO</h1>
       </div>
     </section>
     <section class="u-clearfix u-section-4" id="sec-aed9">
-      <div class="u-clearfix u-sheet u-sheet-1">
+      <div class="u-clearfix u-sheet u-valign-middle u-sheet-1">
         <div class="data-layout-selected u-clearfix u-expanded-width u-gutter-10 u-layout-wrap u-layout-wrap-1">
           <div class="u-gutter-0 u-layout">
             <div class="u-layout-col">
@@ -144,7 +144,7 @@ <h1 class="u-align-center u-text u-text-default u-text-1">TO DO</h1>
                   </div>
                   <div class="u-container-style u-layout-cell u-size-30 u-layout-cell-2">
                     <div class="u-container-layout u-container-layout-2">
-                      <p class="u-text u-text-2"><span class="u-file-icon u-icon u-icon-2"><img src="../images/5291043.png" alt=""></span> The&nbsp;<a href="https://carpentries.org/community-lessons/" target="_blank" class="u-active-none u-border-none u-btn u-button-style u-hover-none u-none u-text-palette-1-base u-btn-2">Carpentries Incubator</a>&nbsp;website contains Carpentries-style teaching materials developed by community members. They offer several R/bioconductor lesson, but in particular the "Introduction to the Bioconductor Project" is one we recommend to get an overview of Bioconductor
+                      <p class="u-text u-text-2"><span class="u-file-icon u-icon u-icon-2"><img src="../images/5291043.png" alt=""></span> The&nbsp;<a href="https://carpentries.org/community-lessons/" target="_blank" class="u-active-none u-border-none u-btn u-button-style u-hover-none u-none u-text-palette-1-base u-btn-2">Carpentries Incubator</a>&nbsp;website contains Carpentries-style teaching materials developed by community members. They offer several R/bioconductor lesson (just type "bioconductor" in the Lesson Title search box), but in particular the "Introduction to the Bioconductor Project" is one we recommend to get an overview of Bioconductor
                       </p>
                       <a href="https://carpentries-incubator.github.io/bioc-project/" class="u-btn u-button-style u-hover-palette-1-dark-1 u-palette-1-base u-btn-3" target="_blank">TAKE THE COURSE</a>
                     </div>
@@ -155,8 +155,7 @@ <h1 class="u-align-center u-text u-text-default u-text-1">TO DO</h1>
                 <div class="u-layout-row">
                   <div class="u-container-style u-layout-cell u-size-30 u-layout-cell-3">
                     <div class="u-container-layout u-container-layout-3">
-                      <p class="u-text u-text-3"><span class="u-file-icon u-icon u-icon-3"><img src="../images/5291043.png" alt=""></span><b>R for Data Science<span style="font-weight: 400;">&nbsp;(chapters 5 to 21) will help you build greater depth to what you le</span>
-                          <span style="font-weight: 400;">arn previously. You will learn how to reshape your data, change names of samples, work with times and dates, or write simple repeatable shortcut functions that will make your R code less bloated</span></b>
+                      <p class="u-text u-text-3"><span class="u-file-icon u-icon u-icon-3"><img src="../images/5291043.png" alt=""></span> If you prefer learning through visuals, Bioconductor has a few short videos available on their YouTube channel that provide a brief introduction to the project
                       </p>
                       <a href="https://www.youtube.com/playlist?list=PLdl4u5ZRDMQSX1YmESUDUIIVBndGM3BMR" class="u-btn u-button-style u-hover-palette-1-dark-1 u-palette-1-base u-btn-4" target="_blank">check the videos</a>
                     </div>

diff --git a/docs/Fundamentals/Bash-Scripting.html b/docs/Fundamentals/Bash-Scripting.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="Bash-Scripting.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/Fundamentals/Basic-R.html b/docs/Fundamentals/Basic-R.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="Basic-R.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/Fundamentals/Fundamentals.html b/docs/Fundamentals/Fundamentals.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="Fundamentals.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/Fundamentals/The-Unix-Shell.html b/docs/Fundamentals/The-Unix-Shell.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="The-Unix-Shell.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/Fundamentals/UCL-Cluster.html b/docs/Fundamentals/UCL-Cluster.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="UCL-Cluster.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/Home.html b/docs/Home.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="Home.css" media="screen">
     <script class="u-script" type="text/javascript" src="jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/NGS_data_analysis/ChIP-Seq.html b/docs/NGS_data_analysis/ChIP-Seq.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="ChIP-Seq.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/NGS_data_analysis/Gene-Expression.html b/docs/NGS_data_analysis/Gene-Expression.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="Gene-Expression.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/NGS_data_analysis/NGS-Data-Analysis.html b/docs/NGS_data_analysis/NGS-Data-Analysis.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="NGS-Data-Analysis.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/NGS_data_analysis/Preprocessing.html b/docs/NGS_data_analysis/Preprocessing.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="Preprocessing.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/NGS_data_analysis/Single-Cell-Gene-Expression.html b/docs/NGS_data_analysis/Single-Cell-Gene-Expression.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="Single-Cell-Gene-Expression.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/NGS_data_analysis/Variant-Calling.html b/docs/NGS_data_analysis/Variant-Calling.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="Variant-Calling.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/Pipelines/Nextflow.html b/docs/Pipelines/Nextflow.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="Nextflow.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/Pipelines/Pipelines.html b/docs/Pipelines/Pipelines.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="Pipelines.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/Pipelines/Using-nf-core-in-Myriad.html b/docs/Pipelines/Using-nf-core-in-Myriad.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="Using-nf-core-in-Myriad.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
     <link id="u-page-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Source+Code+Pro:200,200i,300,300i,400,400i,500,500i,600,600i,700,700i,800,800i,900,900i">
 

diff --git a/docs/Pipelines/nf-core.html b/docs/Pipelines/nf-core.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="nf-core.css" media="screen">
     <script class="u-script" type="text/javascript" src="../jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="../nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">
 
 

diff --git a/docs/index.html b/docs/index.html
@@ -9,7 +9,7 @@
 <link rel="stylesheet" href="Home.css" media="screen">
     <script class="u-script" type="text/javascript" src="jquery.js" defer=""></script>
     <script class="u-script" type="text/javascript" src="nicepage.js" defer=""></script>
-    <meta name="generator" content="Nicepage 5.20.7, nicepage.com">
+    <meta name="generator" content="Nicepage 6.3.1, nicepage.com">
     <link id="u-theme-google-font" rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,100i,300,300i,400,400i,500,500i,700,700i,900,900i|Open+Sans:300,300i,400,400i,500,500i,600,600i,700,700i,800,800i">