Skip to content

Commit

Permalink
Deploy 7a5725d to gh-pages
Browse files Browse the repository at this point in the history
  • Loading branch information
Deploy from CI committed Mar 5, 2024
0 parents commit 1141d7c
Show file tree
Hide file tree
Showing 84 changed files with 11,775 additions and 0 deletions.
49 changes: 49 additions & 0 deletions .github/workflows/deploy.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,49 @@
name: Deploy
on:
push:
branches:
- main

jobs:
deploy:
runs-on: ubuntu-latest
permissions:
contents: write # To push a branch
pull-requests: write # To create a PR from that branch
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- name: Create executable directory
run: |
mkdir mdbook
echo `pwd`/mdbook >> $GITHUB_PATH
- name: Install mdbook
run: |
curl -sSL https://github.com/rust-lang/mdBook/releases/download/v0.4.36/mdbook-v0.4.36-x86_64-unknown-linux-gnu.tar.gz | tar -xz --directory=./mdbook
- name: Install mdbook-toc
run: |
curl -sSL https://github.com/badboy/mdbook-toc/releases/download/0.14.2/mdbook-toc-0.14.2-x86_64-unknown-linux-gnu.tar.gz | tar -xz --directory=./mdbook
- name: Install mdbook-mermaid
run: |
curl -sSL https://github.com/badboy/mdbook-mermaid/releases/download/v0.13.0/mdbook-mermaid-v0.13.0-x86_64-unknown-linux-gnu.tar.gz | tar -xz --directory=./mdbook
# curl -sSL https://raw.githubusercontent.com/badboy/mdbook-mermaid/main/src/bin/assets/mermaid-init.js -o mermaid-init.js
# curl -sSL https://raw.githubusercontent.com/badboy/mdbook-mermaid/main/src/bin/assets/mermaid.min.js -o mermaid.min.js
- name: Deploy GitHub Pages
run: |
# This assumes your book is in the root of your repository.
# Just add a `cd` here if you need to change to another directory.
mdbook-mermaid install .
mdbook build
git worktree add gh-pages
git config user.name "Deploy from CI"
git config user.email ""
cd gh-pages
# Delete the ref to avoid keeping history.
git update-ref -d refs/heads/gh-pages
rm -rf *
mv ../book/html/* .
ls
git add .
git commit -m "Deploy $GITHUB_SHA to gh-pages"
git push --force --set-upstream origin gh-pages
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
book
554 changes: 554 additions & 0 deletions 23fs/fg/01_modern_genomics_i.html

Large diffs are not rendered by default.

305 changes: 305 additions & 0 deletions 23fs/fg/02_modern_genomics_ii.html

Large diffs are not rendered by default.

719 changes: 719 additions & 0 deletions 23fs/fg/03_transcriptomics_i.html

Large diffs are not rendered by default.

417 changes: 417 additions & 0 deletions 23fs/fg/04_transcriptomics_ii.html

Large diffs are not rendered by default.

248 changes: 248 additions & 0 deletions 23fs/fg/functional_genomics.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,248 @@
<!DOCTYPE HTML>
<html lang="en" class="light" dir="ltr">
<head>
<!-- Book generated using mdBook -->
<meta charset="UTF-8">
<title>Functional Genomics - Notes @ ETH Zürich</title>


<!-- Custom HTML head -->

<meta name="description" content="">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="theme-color" content="#ffffff">

<link rel="icon" href="../../favicon.svg">
<link rel="shortcut icon" href="../../favicon.png">
<link rel="stylesheet" href="../../css/variables.css">
<link rel="stylesheet" href="../../css/general.css">
<link rel="stylesheet" href="../../css/chrome.css">
<link rel="stylesheet" href="../../css/print.css" media="print">

<!-- Fonts -->
<link rel="stylesheet" href="../../FontAwesome/css/font-awesome.css">
<link rel="stylesheet" href="../../fonts/fonts.css">

<!-- Highlight.js Stylesheets -->
<link rel="stylesheet" href="../../highlight.css">
<link rel="stylesheet" href="../../tomorrow-night.css">
<link rel="stylesheet" href="../../ayu-highlight.css">

<!-- Custom theme stylesheets -->

<!-- MathJax -->
<script async src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
</head>
<body class="sidebar-visible no-js">
<div id="body-container">
<!-- Provide site root to javascript -->
<script>
var path_to_root = "../../";
var default_theme = window.matchMedia("(prefers-color-scheme: dark)").matches ? "navy" : "light";
</script>

<!-- Work around some values being stored in localStorage wrapped in quotes -->
<script>
try {
var theme = localStorage.getItem('mdbook-theme');
var sidebar = localStorage.getItem('mdbook-sidebar');

if (theme.startsWith('"') && theme.endsWith('"')) {
localStorage.setItem('mdbook-theme', theme.slice(1, theme.length - 1));
}

if (sidebar.startsWith('"') && sidebar.endsWith('"')) {
localStorage.setItem('mdbook-sidebar', sidebar.slice(1, sidebar.length - 1));
}
} catch (e) { }
</script>

<!-- Set the theme before any content is loaded, prevents flash -->
<script>
var theme;
try { theme = localStorage.getItem('mdbook-theme'); } catch(e) { }
if (theme === null || theme === undefined) { theme = default_theme; }
var html = document.querySelector('html');
html.classList.remove('light')
html.classList.add(theme);
var body = document.querySelector('body');
body.classList.remove('no-js')
body.classList.add('js');
</script>

<input type="checkbox" id="sidebar-toggle-anchor" class="hidden">

<!-- Hide / unhide sidebar before it is displayed -->
<script>
var body = document.querySelector('body');
var sidebar = null;
var sidebar_toggle = document.getElementById("sidebar-toggle-anchor");
if (document.body.clientWidth >= 1080) {
try { sidebar = localStorage.getItem('mdbook-sidebar'); } catch(e) { }
sidebar = sidebar || 'visible';
} else {
sidebar = 'hidden';
}
sidebar_toggle.checked = sidebar === 'visible';
body.classList.remove('sidebar-visible');
body.classList.add("sidebar-" + sidebar);
</script>

<nav id="sidebar" class="sidebar" aria-label="Table of contents">
<div class="sidebar-scrollbox">
<ol class="chapter"><li class="chapter-item affix "><a href="../../index.html">Home</a></li><li class="spacer"></li><li class="chapter-item affix "><li class="part-title">22HS</li><li class="chapter-item "><div><strong aria-hidden="true">1.</strong> Computational Biology</div></li><li class="chapter-item "><div><strong aria-hidden="true">2.</strong> Data Mining I</div></li><li class="spacer"></li><li class="chapter-item affix "><li class="part-title">23FS + HS</li><li class="chapter-item "><a href="../../23fs/mham/mobile_health_and_activity_monitoring.html"><strong aria-hidden="true">3.</strong> Mobile Health and Activity Monitoring</a><a class="toggle"><div>❱</div></a></li><li><ol class="section"><li class="chapter-item "><div><strong aria-hidden="true">3.1.</strong> Introduction</div></li></ol></li><li class="chapter-item expanded "><a href="../../23fs/fg/functional_genomics.html" class="active"><strong aria-hidden="true">4.</strong> Functional Genomics</a><a class="toggle"><div>❱</div></a></li><li><ol class="section"><li class="chapter-item "><a href="../../23fs/fg/01_modern_genomics_i.html"><strong aria-hidden="true">4.1.</strong> Modern Genomics I</a></li><li class="chapter-item "><a href="../../23fs/fg/02_modern_genomics_ii.html"><strong aria-hidden="true">4.2.</strong> Modern Genomics II</a></li><li class="chapter-item "><a href="../../23fs/fg/03_transcriptomics_i.html"><strong aria-hidden="true">4.3.</strong> Transcriptomics I</a></li><li class="chapter-item "><a href="../../23fs/fg/04_transcriptomics_ii.html"><strong aria-hidden="true">4.4.</strong> Transcriptomics II</a></li><li class="chapter-item "><div><strong aria-hidden="true">4.5.</strong> MicroRNAs and other small RNAs</div></li><li class="chapter-item "><div><strong aria-hidden="true">4.6.</strong> Proteomics</div></li><li class="chapter-item "><div><strong aria-hidden="true">4.7.</strong> Metabolomics</div></li><li class="chapter-item "><div><strong aria-hidden="true">4.8.</strong> Single Cell Mass Cytometry</div></li><li class="chapter-item "><div><strong aria-hidden="true">4.9.</strong> Protein Networks</div></li><li class="chapter-item "><div><strong aria-hidden="true">4.10.</strong> Epigenomics and Gene Regulation</div></li><li class="chapter-item "><div><strong aria-hidden="true">4.11.</strong> Qualitiy Control and Standards</div></li><li class="spacer"></li></ol></li><li class="chapter-item "><li class="part-title">24FS</li><li class="chapter-item "><div><strong aria-hidden="true">5.</strong> Biofluiddynamics</div></li><li class="chapter-item "><div><strong aria-hidden="true">6.</strong> Synthetic Biology I</div></li></ol>
</div>
<div id="sidebar-resize-handle" class="sidebar-resize-handle">
<div class="sidebar-resize-indicator"></div>
</div>
</nav>

<!-- Track and set sidebar scroll position -->
<script>
var sidebarScrollbox = document.querySelector('#sidebar .sidebar-scrollbox');
sidebarScrollbox.addEventListener('click', function(e) {
if (e.target.tagName === 'A') {
sessionStorage.setItem('sidebar-scroll', sidebarScrollbox.scrollTop);
}
}, { passive: true });
var sidebarScrollTop = sessionStorage.getItem('sidebar-scroll');
sessionStorage.removeItem('sidebar-scroll');
if (sidebarScrollTop) {
// preserve sidebar scroll position when navigating via links within sidebar
sidebarScrollbox.scrollTop = sidebarScrollTop;
} else {
// scroll sidebar to current active section when navigating via "next/previous chapter" buttons
var activeSection = document.querySelector('#sidebar .active');
if (activeSection) {
activeSection.scrollIntoView({ block: 'center' });
}
}
</script>

<div id="page-wrapper" class="page-wrapper">

<div class="page">
<div id="menu-bar-hover-placeholder"></div>
<div id="menu-bar" class="menu-bar sticky">
<div class="left-buttons">
<label id="sidebar-toggle" class="icon-button" for="sidebar-toggle-anchor" title="Toggle Table of Contents" aria-label="Toggle Table of Contents" aria-controls="sidebar">
<i class="fa fa-bars"></i>
</label>
<button id="theme-toggle" class="icon-button" type="button" title="Change theme" aria-label="Change theme" aria-haspopup="true" aria-expanded="false" aria-controls="theme-list">
<i class="fa fa-paint-brush"></i>
</button>
<ul id="theme-list" class="theme-popup" aria-label="Themes" role="menu">
<li role="none"><button role="menuitem" class="theme" id="light">Light</button></li>
<li role="none"><button role="menuitem" class="theme" id="rust">Rust</button></li>
<li role="none"><button role="menuitem" class="theme" id="coal">Coal</button></li>
<li role="none"><button role="menuitem" class="theme" id="navy">Navy</button></li>
<li role="none"><button role="menuitem" class="theme" id="ayu">Ayu</button></li>
</ul>
<button id="search-toggle" class="icon-button" type="button" title="Search. (Shortkey: s)" aria-label="Toggle Searchbar" aria-expanded="false" aria-keyshortcuts="S" aria-controls="searchbar">
<i class="fa fa-search"></i>
</button>
</div>

<h1 class="menu-title">Notes @ ETH Zürich</h1>

<div class="right-buttons">
<a href="../../print.html" title="Print this book" aria-label="Print this book">
<i id="print-button" class="fa fa-print"></i>
</a>

</div>
</div>

<div id="search-wrapper" class="hidden">
<form id="searchbar-outer" class="searchbar-outer">
<input type="search" id="searchbar" name="searchbar" placeholder="Search this book ..." aria-controls="searchresults-outer" aria-describedby="searchresults-header">
</form>
<div id="searchresults-outer" class="searchresults-outer hidden">
<div id="searchresults-header" class="searchresults-header"></div>
<ul id="searchresults">
</ul>
</div>
</div>

<!-- Apply ARIA attributes after the sidebar and the sidebar toggle button are added to the DOM -->
<script>
document.getElementById('sidebar-toggle').setAttribute('aria-expanded', sidebar === 'visible');
document.getElementById('sidebar').setAttribute('aria-hidden', sidebar !== 'visible');
Array.from(document.querySelectorAll('#sidebar a')).forEach(function(link) {
link.setAttribute('tabIndex', sidebar === 'visible' ? 0 : -1);
});
</script>

<div id="content" class="content">
<main>
<h1 id="functional-genomics"><a class="header" href="#functional-genomics">Functional Genomics</a></h1>
<p>A course collectively taught by multiple professors. Multiple-choice exam, lots of memorization.</p>
<h2 id="table-of-contents"><a class="header" href="#table-of-contents">Table of Contents</a></h2>
<ul>
<li><a href="01_modern_genomics_i.html">01. Modern Genomics I</a></li>
<li><a href="02_modern_genomics_ii.html">02. Modern Genomics II</a></li>
<li><a href="03_transcriptomics_i.html">03. Transcriptomics I</a></li>
<li><a href="04_transcriptomics_ii.html">04. Transcriptomics II</a></li>
<li><a href="05_mirnas_and_other_small_rnas.html">05. miRNAs and Other Small RNAs</a></li>
<li><a href="06_proteomics.html">06. Proteomics</a></li>
<li><a href="07_metabolomics.html">07. Metabolomics</a></li>
<li><a href="08_single_cell_mass_cytometry.html">08. Single Cell Mass Cytometry</a></li>
<li><a href="09_protein_networks.html">09. Protein Networks</a></li>
<li><a href="10_epigenomics_and_gene_regulation.html">10. Epigenomics and Gene Regulation</a></li>
<li><a href="11_quality_control_and_standards.html">11. Quality Control and Standards</a></li>
</ul>
<!-- toc -->

</main>

<nav class="nav-wrapper" aria-label="Page navigation">
<!-- Mobile navigation buttons -->
<a rel="prev" href="../../23fs/mham/mobile_health_and_activity_monitoring.html" class="mobile-nav-chapters previous" title="Previous chapter" aria-label="Previous chapter" aria-keyshortcuts="Left">
<i class="fa fa-angle-left"></i>
</a>

<a rel="next prefetch" href="../../23fs/fg/01_modern_genomics_i.html" class="mobile-nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
<i class="fa fa-angle-right"></i>
</a>

<div style="clear: both"></div>
</nav>
</div>
</div>

<nav class="nav-wide-wrapper" aria-label="Page navigation">
<a rel="prev" href="../../23fs/mham/mobile_health_and_activity_monitoring.html" class="nav-chapters previous" title="Previous chapter" aria-label="Previous chapter" aria-keyshortcuts="Left">
<i class="fa fa-angle-left"></i>
</a>

<a rel="next prefetch" href="../../23fs/fg/01_modern_genomics_i.html" class="nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
<i class="fa fa-angle-right"></i>
</a>
</nav>

</div>




<script>
window.playground_copyable = true;
</script>


<script src="../../elasticlunr.min.js"></script>
<script src="../../mark.min.js"></script>
<script src="../../searcher.js"></script>

<script src="../../clipboard.min.js"></script>
<script src="../../highlight.js"></script>
<script src="../../book.js"></script>

<!-- Custom JS scripts -->
<script src="../../mermaid.min.js"></script>
<script src="../../mermaid-init.js"></script>


</div>
</body>
</html>
Binary file added 23fs/fg/img/02-ld-example1.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/02-ld-example2.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/02-nt-diversity.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/03-bowtie.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/03-kmer.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/03-paired-end-seq.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/03-ran-seq-workflow.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/03-read-counting.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/03-rna-prevalence-pie-chart.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/03-rna-selection-method.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/03-rna-seq-experiment-workflow.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/03-rna-species.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/03-star.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/03-tophat2.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/04-20230313162850.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/20240202163019.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/20240202163700.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/20240203111110.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/20240203111302.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/20240203113926.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/20240203113950.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/20240203114453.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/20240203114512.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/20240203114721.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/20240203114758.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added 23fs/fg/img/20240203114809.png
Binary file added 23fs/fg/img/20240203114829.png
Binary file added 23fs/fg/img/20240203134507.png
Binary file added 23fs/fg/img/20240304231416.png
Binary file added 23fs/fg/img/20240304231454.png
Binary file added 23fs/fg/img/20240304231641.png
Binary file added 23fs/fg/img/20240304231833.png
Binary file added 23fs/fg/img/20240305004611.png
Loading

0 comments on commit 1141d7c

Please sign in to comment.