Day 1
2
Lecture 2 - From sequencing reads to expression matrices
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 - Advances in single-cell genomics: the epigenome
13
Lab 7: Single-cell ATAC-seq analysis workflow
14
Lecture 7 - Trajectories and pseudotimes
15
Lab 8: Pseudotime analyses
Day 5
16
Lecture 8 - Advances in single-cell genomics: spatial transcriptomics
Extra resources
2
Lecture 2 - From sequencing reads to expression matrices
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">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-prev"><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:/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_ATAC.html"><span class="chapter-number">12</span> <span class="chapter-title">Lecture 6 - Advances in single-cell genomics: the epigenome</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lab7_atac-seq.html"><span class="chapter-number">13</span> <span class="chapter-title">Lab 7: Single-cell ATAC-seq analysis workflow</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lecture7_pseudotime.html"><span class="chapter-number">14</span> <span class="chapter-title">Lecture 7 - Trajectories and pseudotimes</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lab8_pseudotime.html"><span class="chapter-number">15</span> <span class="chapter-title">Lab 8: Pseudotime analyses</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, F. Almeida-Silva</span> <span class="hidden" data-render-id="footer-right">This book was built with <a href="https://quarto.org/">Quarto</a>.</span> <span class="hidden" data-render-id="quarto-breadcrumbs-faba582bb439d5cd836a674b446052c1">Day 1</span> <span class="hidden" data-render-id="quarto-breadcrumbs-f644ab270ec942bc34c221332a0c9854"><span class="chapter-number">2</span> <span class="chapter-title">Lecture 2 - From sequencing reads to expression matrices</span></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">2</span> <span class="chapter-title">Lecture 2 - From sequencing reads to expression matrices</span></span> <span class="hidden" data-render-id="quarto-twittercardtitle">Single-cell RNAseq analysis with R/Bioconductor - <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-ogcardtitle">Single-cell RNAseq analysis with R/Bioconductor - <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-metasitename">Single-cell RNAseq analysis with R/Bioconductor</span> <span class="hidden" data-render-id="quarto-twittercarddesc"></span> <span class="hidden" data-render-id="quarto-ogcardddesc"></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"); 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