draft outline week 3, omics1

3mmaRand · Sep 3, 2023 · f4f7130 · f4f7130
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diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,5 @@
 .Rdata
 .httr-oauth
 .DS_Store
+
+/.quarto/
diff --git a/_site/index.html b/_site/index.html
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+<html xmlns="http://www.w3.org/1999/xhtml">    
+  <head>      
+    <title>Redirect to about.html</title>      
+    <meta http-equiv="refresh" content="0;URL='about.html'" />    
+  </head>    
+  <body> 
+  </body>  
+</html>     
diff --git a/_site/omics/week-3/study_before_workshop.html b/_site/omics/week-3/study_before_workshop.html
diff --git a/_site/search.json b/_site/search.json
@@ -0,0 +1,51 @@
+[
+  {
+    "objectID": "omics/week-3/study_before_workshop.html#sequence-data",
+    "href": "omics/week-3/study_before_workshop.html#sequence-data",
+    "title": "Independent Study to prepare for workshop",
+    "section": "Sequence Data",
+    "text": "Sequence Data\n\nreads\nquality control\nalign/pseudoalign\nquantify\nnormalise"
+  },
+  {
+    "objectID": "omics/week-3/study_before_workshop.html#aims",
+    "href": "omics/week-3/study_before_workshop.html#aims",
+    "title": "Independent Study to prepare for workshop",
+    "section": "Aims",
+    "text": "Aims\n\nfind important genes\nwhat is ‘important’\n\nexpressed\ndifferentially expressed i.e., which genes are significantly higher in one group vs another"
+  },
+  {
+    "objectID": "omics/week-3/study_before_workshop.html#what-is-a-read",
+    "href": "omics/week-3/study_before_workshop.html#what-is-a-read",
+    "title": "Independent Study to prepare for workshop",
+    "section": "What is a read",
+    "text": "What is a read"
+  },
+  {
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+    "href": "omics/week-3/study_before_workshop.html#stem-cells",
+    "title": "Independent Study to prepare for workshop",
+    "section": "Stem cells",
+    "text": "Stem cells\n\nRaw data: GEO Series GSE81682\nIllumina HiSeq\nshort reads 150-300bp\nA single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation (Nestorowa et al. 2016)"
+  },
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+    "href": "omics/week-3/study_before_workshop.html#differential-expression",
+    "title": "Independent Study to prepare for workshop",
+    "section": "Differential expression",
+    "text": "Differential expression\n\nwhat is differentially expressed\nhow are DE genes related\nwhat are DE genes involved with"
+  },
+  {
+    "objectID": "omics/week-3/study_before_workshop.html#processing-so-far",
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+    "section": "Processing so far",
+    "text": "Processing so far"
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+    "href": "omics/week-3/study_before_workshop.html#section-2",
+    "title": "Independent Study to prepare for workshop",
+    "section": "",
+    "text": "Nestorowa, Sonia, Fiona K. Hamey, Blanca Pijuan Sala, Evangelia Diamanti, Mairi Shepherd, Elisa Laurenti, Nicola K. Wilson, David G. Kent, and Berthold Göttgens. 2016. “A Single-Cell Resolution Map of Mouse Hematopoietic Stem and Progenitor Cell Differentiation.” Blood 128 (8): e20–31. https://doi.org/10.1182/blood-2016-05-716480."
+  }
+]
diff --git a/_site/site_libs/clipboard/clipboard.min.js b/_site/site_libs/clipboard/clipboard.min.js
diff --git a/_site/site_libs/quarto-html/light-border.css b/_site/site_libs/quarto-html/light-border.css
diff --git a/_site/site_libs/quarto-html/popper.min.js b/_site/site_libs/quarto-html/popper.min.js
diff --git a/_site/site_libs/quarto-html/quarto-html.min.css b/_site/site_libs/quarto-html/quarto-html.min.css
diff --git a/_site/site_libs/quarto-html/quarto-syntax-highlighting.css b/_site/site_libs/quarto-html/quarto-syntax-highlighting.css