Deploying to gh-pages from @ 624bf40 🚀

core/core.html

@@ -173,25 +173,25 @@
       <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="../core/week-2/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-2/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../core/week-2/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-2/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../core/week-2/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-2/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../core/week-2/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-2/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
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       <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="../core/week-6/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../core/week-6/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../core/week-6/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
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           <li class="sidebar-item">
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-  <a href="../core/week-6/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
@@ -245,9 +245,9 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#content" id="toc-content" class="nav-link active" data-scroll-target="#content">Content</a>
   <ul class="collapse">
-  <li><a href="#core-1" id="toc-core-1" class="nav-link" data-scroll-target="#core-1">Core 1</a></li>
-  <li><a href="#core-2" id="toc-core-2" class="nav-link" data-scroll-target="#core-2">Core 2</a></li>
-  <li><a href="#core-3-quarto" id="toc-core-3-quarto" class="nav-link" data-scroll-target="#core-3-quarto">Core 3: Quarto</a></li>
+  <li><a href="#week-1-core-1-organising-reproducible-data-analyses" id="toc-week-1-core-1-organising-reproducible-data-analyses" class="nav-link" data-scroll-target="#week-1-core-1-organising-reproducible-data-analyses">Week 1 Core 1 Organising Reproducible Data Analyses</a></li>
+  <li><a href="#week-2-core-2-needs-a-title" id="toc-week-2-core-2-needs-a-title" class="nav-link" data-scroll-target="#week-2-core-2-needs-a-title">Week 2 Core 2 NEEDS A TITLE</a></li>
+  <li><a href="#week-6-core-3-reproducible-reporting" id="toc-week-6-core-3-reproducible-reporting" class="nav-link" data-scroll-target="#week-6-core-3-reproducible-reporting">Week 6 Core 3 Reproducible Reporting</a></li>
   </ul></li>
   </ul>
 </nav>
@@ -274,32 +274,50 @@ <h1 class="title">Core Data Analysis for Group Project</h1>
 
 <section id="content" class="level1">
 <h1>Content</h1>
-<section id="core-1" class="level2">
-<h2 class="anchored" data-anchor-id="core-1">Core 1</h2>
-<p>Note no R coding (too early for 70M)</p>
+<p>Overview You are either an integrated masters student doing 88H Group Project or a MSc Bioinformatics student doing 70M</p>
+<section id="week-1-core-1-organising-reproducible-data-analyses" class="level2">
+<h2 class="anchored" data-anchor-id="week-1-core-1-organising-reproducible-data-analyses">Week 1 Core 1 Organising Reproducible Data Analyses</h2>
+<p>Note no R coding (too early for MSc BIN 70M who share the core and omics teaching)</p>
+<p>Before - Optional revision: What they forgot to teach you about computers: operating systems, file systems, file types, working directories and paths</p>
+<ul>
+<li>Why reproducibility (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown)</li>
+</ul>
+<p>Workshop</p>
 <ul>
 <li>Project organisation: folders, files</li>
 <li>Project oriented workflow</li>
-<li>Readme</li>
 <li>Naming things</li>
-<li>Keeping notes</li>
-<li>Data management, google drive: https://www.york.ac.uk/it-services/services/drive/#tab-6</li>
-<li>file formats</li>
-<li>Introduction to data in general. Similarities and differences
+<li>File formats</li>
+<li>Data management
+<ul>
+<li>google drive: https://www.york.ac.uk/it-services/services/drive/#tab-6</li>
+<li>documenting</li>
+<li>organisation within files</li>
+</ul></li>
+<li>Data files. Similarities and differences
 <ul>
 <li>Sequences data</li>
 <li>Image data</li>
 <li>Structure data.</li>
 </ul></li>
+<li>Keeping notes</li>
+<li>Readme</li>
+<li>Reference managers: Zotero</li>
 </ul>
+<p>After</p>
 </section>
-<section id="core-2" class="level2">
-<h2 class="anchored" data-anchor-id="core-2">Core 2</h2>
-<p>rgetgretger</p>
+<section id="week-2-core-2-needs-a-title" class="level2">
+<h2 class="anchored" data-anchor-id="week-2-core-2-needs-a-title">Week 2 Core 2 NEEDS A TITLE</h2>
+<p>Before Possibly: Code formatting and style, 😎 Cool code Tips, Code ‘algorithmically.’, Writing functions (R and python??) (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown)</p>
+<p>Workshop</p>
+<p>After</p>
 </section>
-<section id="core-3-quarto" class="level2">
-<h2 class="anchored" data-anchor-id="core-3-quarto">Core 3: Quarto</h2>
-<p>fgzzdfghdfhg</p>
+<section id="week-6-core-3-reproducible-reporting" class="level2">
+<h2 class="anchored" data-anchor-id="week-6-core-3-reproducible-reporting">Week 6 Core 3 Reproducible Reporting</h2>
+<p>Before (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown and BIO00058M-Data-science-2020/slides/04_advanced_rmarkdown.html) Literate programming What is quarto markdown basics: text, code chunks, headings yaml automatic numbering of figures and tables cross references special characters citations</p>
+<p>Workshop</p>
+<p>practice doing the above with your project and data</p>
+<p>After</p>
 
 
 </section>

core/week-1/overview.html

@@ -173,25 +173,25 @@
       <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="../../core/week-2/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
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       <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="../../core/week-6/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
@@ -245,7 +245,7 @@
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
 <h1 class="title">Overview</h1>
-<p class="subtitle lead">Core 1</p>
+<p class="subtitle lead">Core 1: Organising Data Analyses</p>
 </div>
 
 
@@ -275,7 +275,7 @@ <h3 class="anchored" data-anchor-id="instructions">Instructions</h3>
 <ol type="1">
 <li><p><a href="../../core/week-1/study_before_workshop.html">Prepare</a></p>
 <ol type="i">
-<li>📖 Read ddd</li>
+<li>📖 Read <a href="https://3mmarand.github.io/comp4biosci/what_they_forgot.html">What they forgot to teach you about computers</a></li>
 </ol></li>
 <li><p><a href="../../core/week-1/workshop.html">Workshop</a></p>
 <ol type="i">

core/week-1/study_after_workshop.html

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           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
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       <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="../../core/week-6/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
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           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>

core/week-1/study_before_workshop.html

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           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-2/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-2/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>
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       <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="../../core/week-6/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">About</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Prepare!</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Workshop</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../../core/week-6/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
 </li>