12
Lecture 6 - Trajectories and pseudotimes
Single-cell RNAseq analysis with R/Bioconductor
Welcome
Program
RStudio
Prerequisites
Day 1
1
Lecture 1 - Introduction to scRNAseq analysis
2
Lecture 2 - From sequencing reads to expression matrices
3
Lab 1: Familiarizing yourself with the course AWS instance
4
Lab 2: From .bcl to count matrix
Day 2
5
Lecture 3 - Quality control for scRNA-Seq data
6
Lab 3: Introduction to R/Bioconductor
7
Lab 4 - Single-cell RNA-seq data wrangling
Day 3
8
Lecture 4 - Identifying cell populations
9
Lab 5: Dimension reduction, clustering and annotation
10
Lecture 5 - Data integration and batch effect correction
11
Lab 6 - Batch correction
Day 4
12
Lecture 6 - Trajectories and pseudotimes
13
Lab 7: Pseudotime analyses
14
Lecture 7 - Advances in single-cell genomics: the epigenome
15
Lab 8 - Single-cell ATAC-seq analysis workflow
Day 5
16
Lecture 8 - Advances in single-cell genomics: spatial transcriptomics
Extra resources
12
Lecture 6 - Trajectories and pseudotimes
Slides here
<div id="quarto-navigation-envelope" class="hidden"> <p><span class="hidden" data-render-id="quarto-int-sidebar-title">Single-cell RNAseq analysis with R/Bioconductor</span> <span class="hidden" data-render-id="quarto-int-navbar-title">Single-cell RNAseq analysis with R/Bioconductor</span> <span class="hidden" data-render-id="quarto-int-next"><span class="chapter-number">13</span> <span class="chapter-title">Lab 7: Pseudotime analyses</span></span> <span class="hidden" data-render-id="quarto-int-prev"><span class="chapter-number">11</span> <span class="chapter-title">Lab 6 - Batch correction</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/index.html">Welcome</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/program.html">Program</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/Rstudio.html">RStudio</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/prerequisites.html">Prerequisites</span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-1">Day 1</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lecture1_introduction.html"><span class="chapter-number">1</span> <span class="chapter-title">Lecture 1 - Introduction to scRNAseq analysis</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lecture2_Bcl2matrix.html"><span class="chapter-number">2</span> <span class="chapter-title">Lecture 2 - From sequencing reads to expression matrices</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lab1_Intro.html"><span class="chapter-number">3</span> <span class="chapter-title">Lab 1: Familiarizing yourself with the course AWS instance</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lab2_processingreads.html"><span class="chapter-number">4</span> <span class="chapter-title">Lab 2: From .bcl to count matrix</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-2">Day 2</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Lecture3_qualitycontrol.html"><span class="chapter-number">5</span> <span class="chapter-title">Lecture 3 - Quality control for scRNA-Seq data</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Lab3_Rbioc.html"><span class="chapter-number">6</span> <span class="chapter-title">Lab 3: Introduction to R/Bioconductor</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Lab4_data_wrangling_scRNAseq.html"><span class="chapter-number">7</span> <span class="chapter-title">Lab 4 - Single-cell RNA-seq data wrangling</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-3">Day 3</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Lecture4_clustering.html"><span class="chapter-number">8</span> <span class="chapter-title">Lecture 4 - Identifying cell populations</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Lab5_clustering.html"><span class="chapter-number">9</span> <span class="chapter-title">Lab 5: Dimension reduction, clustering and annotation</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Lecture5_batchcorrection.html"><span class="chapter-number">10</span> <span class="chapter-title">Lecture 5 - Data integration and batch effect correction</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Lab6_batch_correction.html"><span class="chapter-number">11</span> <span class="chapter-title">Lab 6 - Batch correction</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-4">Day 4</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lecture6_pseudotime.html"><span class="chapter-number">12</span> <span class="chapter-title">Lecture 6 - Trajectories and pseudotimes</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lab7_pseudotime.html"><span class="chapter-number">13</span> <span class="chapter-title">Lab 7: Pseudotime analyses</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lecture7_ATAC.html"><span class="chapter-number">14</span> <span class="chapter-title">Lecture 7 - Advances in single-cell genomics: the epigenome</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lab8_atac-seq.html"><span class="chapter-number">15</span> <span class="chapter-title">Lab 8 - Single-cell ATAC-seq analysis workflow</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-5">Day 5</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day5/Lecture8_spatial-transcriptomics.html"><span class="chapter-number">16</span> <span class="chapter-title">Lecture 8 - Advances in single-cell genomics: spatial transcriptomics</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/extra.html">Extra resources</span> <span class="hidden" data-render-id="footer-left">Single-cell RNAseq analysis with R/Bioconductor |<br /> J. Serizay O. Ashenberg</span> <span class="hidden" data-render-id="footer-right">This book was built with <a href="https://quarto.org/">Quarto</a>.</span></p> </div> <div id="quarto-meta-markdown" class="hidden"> <p><span class="hidden" data-render-id="quarto-metatitle">Single-cell RNAseq analysis with R/Bioconductor - <span class="chapter-number">12</span> <span class="chapter-title">Lecture 6 - Trajectories and pseudotimes</span></span> <span class="hidden" data-render-id="quarto-twittercardtitle">Single-cell RNAseq analysis with R/Bioconductor - <span class="chapter-number">12</span> <span class="chapter-title">Lecture 6 - Trajectories and pseudotimes</span></span> <span class="hidden" data-render-id="quarto-ogcardtitle">Single-cell RNAseq analysis with R/Bioconductor - <span class="chapter-number">12</span> <span class="chapter-title">Lecture 6 - Trajectories and pseudotimes</span></span> <span class="hidden" data-render-id="quarto-metasitename">Single-cell RNAseq analysis with R/Bioconductor</span></p> </div> </main> <!-- /main --> <script id = "quarto-html-after-body" type="application/javascript"> window.document.addEventListener("DOMContentLoaded", function (event) { const toggleBodyColorMode = (bsSheetEl) => { const mode = bsSheetEl.getAttribute("data-mode"); const bodyEl = window.document.querySelector("body"); if (mode === "dark") { bodyEl.classList.add("quarto-dark"); bodyEl.classList.remove("quarto-light"); } else { bodyEl.classList.add("quarto-light"); bodyEl.classList.remove("quarto-dark"); } } const toggleBodyColorPrimary = () => { const bsSheetEl = window.document.querySelector("link#quarto-bootstrap"); if (bsSheetEl) { toggleBodyColorMode(bsSheetEl); } } toggleBodyColorPrimary(); const icon = ""; const anchorJS = new window.AnchorJS(); anchorJS.options = { placement: 'right', icon: icon }; anchorJS.add('.anchored'); const clipboard = new window.ClipboardJS('.code-copy-button', { target: function(trigger) { return trigger.previousElementSibling; } }); clipboard.on('success', function(e) { // button target const button = e.trigger; // don't keep focus button.blur(); // flash "checked" button.classList.add('code-copy-button-checked'); var currentTitle = button.getAttribute("title"); button.setAttribute("title", "Copied!"); setTimeout(function() { button.setAttribute("title", currentTitle); button.classList.remove('code-copy-button-checked'); }, 1000); // clear code selection e.clearSelection(); }); function tippyHover(el, contentFn) { const config = { allowHTML: true, content: contentFn, maxWidth: 500, delay: 100, arrow: false, appendTo: function(el) { return el.parentElement; }, interactive: true, interactiveBorder: 10, theme: 'quarto', placement: 'bottom-start' }; window.tippy(el, config); } const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]'); for (var i=0; i<noterefs.length; i++) { const ref = noterefs[i]; tippyHover(ref, function() { // use id or data attribute instead here let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href'); try { href = new URL(href).hash; } catch {} const id = href.replace(/^#\/?/, ""); const note = window.document.getElementById(id); return note.innerHTML; }); } var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]'); for (var i=0; i<bibliorefs.length; i++) { const ref = bibliorefs[i]; const cites = ref.parentNode.getAttribute('data-cites').split(' '); tippyHover(ref, function() { var popup = window.document.createElement('div'); cites.forEach(function(cite) { var citeDiv = window.document.createElement('div'); citeDiv.classList.add('hanging-indent'); citeDiv.classList.add('csl-entry'); var biblioDiv = window.document.getElementById('ref-' + cite); if (biblioDiv) { citeDiv.innerHTML = biblioDiv.innerHTML; } popup.appendChild(citeDiv); }); return popup.innerHTML; }); } }); </script> <nav class="page-navigation"> <div class="nav-page nav-page-previous"> <a href="/content/day3/Lab6_batch_correction.html" class="pagination-link"> <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class='chapter-number'>11</span> <span class='chapter-title'>Lab 6 - Batch correction</span></span> </a> </div> <div class="nav-page nav-page-next"> <a href="/content/day4/Lab7_pseudotime.html" class="pagination-link"> <span class="nav-page-text"><span class='chapter-number'>13</span> <span class='chapter-title'>Lab 7: Pseudotime analyses</span></span> <i class="bi bi-arrow-right-short"></i> </a> </div> </nav> </div> <!-- /content --> <footer class="footer"> <div class="nav-footer"> <div class="nav-footer-left"> <div class='footer-contents'>Single-cell RNAseq analysis with R/Bioconductor | J. 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