Deploying to gh-pages from @ f4f7130 🚀

core/core.html

@@ -299,9 +299,9 @@ <h2 class="anchored" data-anchor-id="week-1-core-1-organising-reproducible-data-
 <li>Image data</li>
 <li>Structure data.</li>
 </ul></li>
-<li>Keeping notes</li>
+<li>Keeping a lab book</li>
 <li>Readme</li>
-<li>Reference managers: Zotero</li>
+<li>Reference managers: Zotero?</li>
 </ul>
 <p>After</p>
 </section>

omics/data/betsy/meta_data.txt

@@ -0,0 +1,19 @@
+sample_id stage treatment sibling_rep
+S14_C_5 stage_14 control five
+S14_C_6 stage_14 control six
+S14_C_A stage_14 control A
+S14_F_5 stage_14 FGF five
+S14_F_6 stage_14 FGF six
+S14_F_A stage_14 FGF A
+S20_C_5 stage_20 control five
+S20_C_6 stage_20 control six
+S20_C_A stage_20 control A
+S20_F_5 stage_20 FGF five
+S20_F_6 stage_20 FGF six
+S20_F_A stage_20 FGF A
+S30_C_5 stage_30 control five
+S30_C_6 stage_30 control six
+S30_C_A stage_30 control A
+S30_F_5 stage_30 FGF five
+S30_F_6 stage_30 FGF six
+S30_F_A stage_30 FGF A

omics/omics.html

@@ -137,25 +137,25 @@
       <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../omics/week-3/overview.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../omics/week-3/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="../omics/week-3/study_before_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../omics/week-3/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="../omics/week-3/workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../omics/week-3/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="../omics/week-3/study_after_workshop.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../omics/week-3/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="#omics-1" id="toc-omics-1" class="nav-link" data-scroll-target="#omics-1">Omics 1</a></li>
-  <li><a href="#omics-2" id="toc-omics-2" class="nav-link" data-scroll-target="#omics-2">Omics 2</a></li>
-  <li><a href="#omics-3" id="toc-omics-3" class="nav-link" data-scroll-target="#omics-3">Omics 3</a></li>
+  <li><a href="#omics-1-hello-data" id="toc-omics-1-hello-data" class="nav-link" data-scroll-target="#omics-1-hello-data">Omics 1: Hello data!</a></li>
+  <li><a href="#omics-2-statisitcal-analysis" id="toc-omics-2-statisitcal-analysis" class="nav-link" data-scroll-target="#omics-2-statisitcal-analysis">Omics 2: Statisitcal Analysis</a></li>
+  <li><a href="#omics-3-visualising-and-interpreting" id="toc-omics-3-visualising-and-interpreting" class="nav-link" data-scroll-target="#omics-3-visualising-and-interpreting">Omics 3: Visualising and Interpreting</a></li>
   </ul></li>
   </ul>
 </nav>
@@ -274,17 +274,23 @@ <h1 class="title">Omics Data Analysis for Group Project</h1>
 
 <section id="content" class="level1">
 <h1>Content</h1>
-<section id="omics-1" class="level2">
-<h2 class="anchored" data-anchor-id="omics-1">Omics 1</h2>
-<p>erwtERTERTG</p>
+<section id="omics-1-hello-data" class="level2">
+<h2 class="anchored" data-anchor-id="omics-1-hello-data">Omics 1: Hello data!</h2>
+<p>before - sequence data fundamentals - where have the data come from - processing so far - why log2 - overarching aims</p>
+<p>workshop - set up a project and create the organisation - meta data - open in understanding the data numbers of variables, organisation - importing - exploring, what kind of values are they, how many missing - qc plots - removing the useless, writing to files</p>
+<p>after - document what you have done - format your figures</p>
 </section>
-<section id="omics-2" class="level2">
-<h2 class="anchored" data-anchor-id="omics-2">Omics 2</h2>
-<p>rgetgretger</p>
+<section id="omics-2-statisitcal-analysis" class="level2">
+<h2 class="anchored" data-anchor-id="omics-2-statisitcal-analysis">Omics 2: Statisitcal Analysis</h2>
+<p>before - which genes matter: expression, DE - goal of DE - how does DE work - multiple testing: FDR - say what comparisons we will do</p>
+<p>workshop - open project import the data - revise! - prep for DE - lists of genes - writing to files</p>
+<p>after - document what you have done - repeat on another comparison</p>
 </section>
-<section id="omics-3" class="level2">
-<h2 class="anchored" data-anchor-id="omics-3">Omics 3</h2>
-<p>fgzzdfghdfhg</p>
+<section id="omics-3-visualising-and-interpreting" class="level2">
+<h2 class="anchored" data-anchor-id="omics-3-visualising-and-interpreting">Omics 3: Visualising and Interpreting</h2>
+<p>before - recap what we have - volcano plot described - GO terms -</p>
+<p>workshop - open project import the data - revise! - volcano plot - kable table? knitr::kable(df) |&gt; kableExtra::kable_styling() - annotating with go terms</p>
+<p>after - document what you have done - repeat on another comparison</p>
 
 
 </section>