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Quarto GHA Workflow Runner committed May 1, 2024
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2 changes: 1 addition & 1 deletion .nojekyll
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241 changes: 213 additions & 28 deletions course_schedule.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.3.361">
<meta name="generator" content="quarto-1.4.553">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">


<title>Spatial transcriptomics – course_schedule</title>
<title>Spatial transcriptomics</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
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"collapse-after": 3,
"panel-placement": "end",
"type": "overlay",
"limit": 20,
"limit": 50,
"keyboard-shortcut": [
"f",
"/",
"s"
],
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"language": {
"search-no-results-text": "No results",
"search-matching-documents-text": "matching documents",
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"search-more-match-text": "more match in this document",
"search-more-matches-text": "more matches in this document",
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"search-text-placeholder": "",
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"search-submit-button-title": "Submit",
"search-label": "Search"
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<div id="quarto-search-results"></div>
<header id="quarto-header" class="headroom fixed-top">
<nav class="navbar navbar-expand-lg navbar-dark ">
<nav class="navbar navbar-expand-lg " data-bs-theme="dark">
<div class="navbar-container container-fluid">
<div class="navbar-brand-container">
<div class="navbar-brand-container mx-auto">
<a class="navbar-brand" href="./index.html">
<span class="navbar-title">Spatial transcriptomics</span>
</a>
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<div class="collapse navbar-collapse" id="navbarCollapse">
<ul class="navbar-nav navbar-nav-scroll me-auto">
<li class="nav-item">
<a class="nav-link active" href="./index.html" rel="" target="" aria-current="page">
<span class="menu-text">Home</span></a>
<a class="nav-link active" href="./index.html" aria-current="page">
<span class="menu-text">Home</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="./precourse_preparations.html" rel="" target="">
<span class="menu-text">Pre-course preparations</span></a>
<a class="nav-link" href="./precourse_preparations.html">
<span class="menu-text">Pre-course preparations</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="./course_schedule.html" rel="" target="">
<span class="menu-text">Course schedule</span></a>
<a class="nav-link" href="./course_schedule.html">
<span class="menu-text">Course schedule</span></a>
</li>
<li class="nav-item dropdown ">
<a class="nav-link dropdown-toggle" href="#" id="nav-menu-course-material" role="button" data-bs-toggle="dropdown" aria-expanded="false" rel="" target="">
<a class="nav-link dropdown-toggle" href="#" id="nav-menu-course-material" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="menu-text">Course material</span>
</a>
<ul class="dropdown-menu" aria-labelledby="nav-menu-course-material">
<li>
<a class="dropdown-item" href="./quality_control.html" rel="" target="">
<a class="dropdown-item" href="./quality_control.html">
<span class="dropdown-text">Quality control</span></a>
</li>
<li>
<a class="dropdown-item" href="./normalization_scaling.html" rel="" target="">
<a class="dropdown-item" href="./normalization_scaling.html">
<span class="dropdown-text">Normalization and scaling</span></a>
</li>
</ul>
</li>
</ul>
<ul class="navbar-nav navbar-nav-scroll ms-auto">
<li class="nav-item compact">
<a class="nav-link" href="https://github.com/sib-swiss/single-cell-python-training/" rel="" target=""><i class="bi bi-github" role="img" aria-label="GitHub">
<a class="nav-link" href="https://github.com/sib-swiss/single-cell-python-training/"> <i class="bi bi-github" role="img" aria-label="GitHub">
</i>
<span class="menu-text"></span></a>
<span class="menu-text"></span></a>
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<div class="quarto-navbar-tools">
</div>
</div> <!-- /navcollapse -->
<div class="quarto-navbar-tools">
</div>
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</nav>
<nav class="quarto-secondary-nav">
<div class="container-fluid d-flex">
<button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
<button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
<i class="bi bi-layout-text-sidebar-reverse"></i>
</button>
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"></ol></nav>
<a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
</a>
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"></ol></nav>
<a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
</a>
</div>
</nav>
</header>
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<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
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<nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
<nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
<div class="pt-lg-2 mt-2 text-left sidebar-header">
<a href="./index.html" class="sidebar-logo-link">
<img src="./assets/SIB_LogoQ_GBv.svg" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
</a>
</div>
</nav>
<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
<!-- margin-sidebar -->
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">

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</main> <!-- /main -->
<script id="quarto-html-after-body" type="application/javascript">
window.document.addEventListener("DOMContentLoaded", function (event) {
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// clear code selection
e.clearSelection();
});
function tippyHover(el, contentFn) {
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp("https:\/\/sib-swiss\.github\.io\/single-cell-python-training\/");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
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const link = links[i];
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if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
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content: contentFn,
maxWidth: 500,
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arrow: false,
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interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start'
placement: 'bottom-start',
};
if (contentFn) {
config.content = contentFn;
}
if (onTriggerFn) {
config.onTrigger = onTriggerFn;
}
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config.onUntrigger = onUntriggerFn;
}
window.tippy(el, config);
}
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
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try { href = new URL(href).hash; } catch {}
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return note.innerHTML;
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return "";
}
});
}
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// Strip column container classes
const stripColumnClz = (el) => {
el.classList.remove("page-full", "page-columns");
if (el.children) {
for (const child of el.children) {
stripColumnClz(child);
}
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stripColumnClz(note)
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if (note.children && note.children.length > 2) {
container.appendChild(note.children[0].cloneNode(true));
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const child = note.children[i];
if (child.tagName === "P" && child.innerText === "") {
continue;
} else {
container.appendChild(child.cloneNode(true));
break;
}
}
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(container);
}
return container.innerHTML
} else {
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(note);
}
return note.innerHTML;
}
} else {
// Remove any anchor links if they are present
const anchorLink = note.querySelector('a.anchorjs-link');
if (anchorLink) {
anchorLink.remove();
}
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(note);
}
// TODO in 1.5, we should make sure this works without a callout special case
if (note.classList.contains("callout")) {
return note.outerHTML;
} else {
return note.innerHTML;
}
}
}
for (var i=0; i<xrefs.length; i++) {
const xref = xrefs[i];
tippyHover(xref, undefined, function(instance) {
instance.disable();
let url = xref.getAttribute('href');
let hash = undefined;
if (url.startsWith('#')) {
hash = url;
} else {
try { hash = new URL(url).hash; } catch {}
}
if (hash) {
const id = hash.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
if (note !== null) {
try {
const html = processXRef(id, note.cloneNode(true));
instance.setContent(html);
} finally {
instance.enable();
instance.show();
}
} else {
// See if we can fetch this
fetch(url.split('#')[0])
.then(res => res.text())
.then(html => {
const parser = new DOMParser();
const htmlDoc = parser.parseFromString(html, "text/html");
const note = htmlDoc.getElementById(id);
if (note !== null) {
const html = processXRef(id, note);
instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
} else {
// See if we can fetch a full url (with no hash to target)
// This is a special case and we should probably do some content thinning / targeting
fetch(url)
.then(res => res.text())
.then(html => {
const parser = new DOMParser();
const htmlDoc = parser.parseFromString(html, "text/html");
const note = htmlDoc.querySelector('main.content');
if (note !== null) {
// This should only happen for chapter cross references
// (since there is no id in the URL)
// remove the first header
if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
note.children[0].remove();
}
const html = processXRef(null, note);
instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
}, function(instance) {
});
}
let selectedAnnoteEl;
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}
div.style.top = top - 2 + "px";
div.style.height = height + 4 + "px";
div.style.left = 0;
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
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gutterDiv = window.document.createElement("div");
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});
selectedAnnoteEl = undefined;
};
// Handle positioning of the toggle
window.addEventListener(
"resize",
throttle(() => {
elRect = undefined;
if (selectedAnnoteEl) {
selectCodeLines(selectedAnnoteEl);
}
}, 10)
);
function throttle(fn, ms) {
let throttle = false;
let timer;
return (...args) => {
if(!throttle) { // first call gets through
fn.apply(this, args);
throttle = true;
} else { // all the others get throttled
if(timer) clearTimeout(timer); // cancel #2
timer = setTimeout(() => {
fn.apply(this, args);
timer = throttle = false;
}, ms);
}
};
}
// Attach click handler to the DT
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
for (const annoteDlNode of annoteDls) {
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</body></html>
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