Day 2
6
Lecture 4 - ATAC-seq processing and analyis
Epigenomics Data Analysis
Welcome
Program
RStudio
Prerequisites
Day 1
1
Lecture 1 - Introduction to epigenomics data analysis
2
Lecture 2 - General processing of genome-wide epigenomic assays
3
Demo 1 - Processing of MNase-seq data
4
Lab 1 - Processing of MNase-seq data
Day 2
5
Lecture 3 - NGS processing workflows
6
Lecture 4 - ATAC-seq processing and analyis
7
Lecture 5 - R 101
8
Demo 2 - Processing of ATAC-seq data
9
Lab 2 - ATAC-seq downstream analysis
Day 3
10
Lecture 6 - ChIP-seq processing and analyis
11
Lecture 7 - R 201
12
Demo 3 - Processing of ChIP-seq data
13
Lab 3 - ChIP-seq downstream analysis
Day 4
14
Lecture 8 - RNA-seq processing and analyis
15
Lecture 9 - R 301
16
Demo 4 - Processing of RNA-seq data
17
Lab 4 - RNA-seq downstream analysis
Day 5
18
Lecture 10 - HiC processing
19
Lecture 11 - GO and GSEA analysis
20
Demo 5 - Leveraging Bioconductor resources
21
Lab 5 - Multi-omics data integration
Extra resources
6
Lecture 4 - ATAC-seq processing and analyis
<div id="quarto-navigation-envelope" class="hidden"> <p><span class="hidden" data-render-id="quarto-int-sidebar-title">Epigenomics Data Analysis</span> <span class="hidden" data-render-id="quarto-int-navbar-title">Epigenomics Data Analysis</span> <span class="hidden" data-render-id="quarto-int-next"><span class="chapter-number">7</span> <span class="chapter-title">Lecture 5 - R 101</span></span> <span class="hidden" data-render-id="quarto-int-prev"><span class="chapter-number">5</span> <span class="chapter-title">Lecture 3 - NGS processing workflows</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 epigenomics data analysis</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lecture2_processing.html"><span class="chapter-number">2</span> <span class="chapter-title">Lecture 2 - General processing of genome-wide epigenomic assays</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Demo1_MNase-seq_processing.html"><span class="chapter-number">3</span> <span class="chapter-title">Demo 1 - Processing of MNase-seq data</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lab1_MNase-seq_processing.html"><span class="chapter-number">4</span> <span class="chapter-title">Lab 1 - Processing of MNase-seq data</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_workflows.html"><span class="chapter-number">5</span> <span class="chapter-title">Lecture 3 - NGS processing workflows</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Lecture4_ATACseq.html"><span class="chapter-number">6</span> <span class="chapter-title">Lecture 4 - ATAC-seq processing and analyis</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Lecture5_R-101.html"><span class="chapter-number">7</span> <span class="chapter-title">Lecture 5 - R 101</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Demo2_ATAC-seq_processing.html"><span class="chapter-number">8</span> <span class="chapter-title">Demo 2 - Processing of ATAC-seq data</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Lab2_ATAC-seq_analysis.html"><span class="chapter-number">9</span> <span class="chapter-title">Lab 2 - ATAC-seq downstream analysis</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/Lecture6_ChIPseq.html"><span class="chapter-number">10</span> <span class="chapter-title">Lecture 6 - ChIP-seq processing and analyis</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Lecture7_R-201.html"><span class="chapter-number">11</span> <span class="chapter-title">Lecture 7 - R 201</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Demo3_ChIP-seq_processing.html"><span class="chapter-number">12</span> <span class="chapter-title">Demo 3 - Processing of ChIP-seq data</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Lab3_ChIP-seq_analysis.html"><span class="chapter-number">13</span> <span class="chapter-title">Lab 3 - ChIP-seq downstream analysis</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/Lecture8_RNAseq.html"><span class="chapter-number">14</span> <span class="chapter-title">Lecture 8 - RNA-seq processing and analyis</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lecture9_R-301.html"><span class="chapter-number">15</span> <span class="chapter-title">Lecture 9 - R 301</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Demo4_RNA-seq_processing.html"><span class="chapter-number">16</span> <span class="chapter-title">Demo 4 - Processing of RNA-seq data</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lab4_RNA-seq_analysis.html"><span class="chapter-number">17</span> <span class="chapter-title">Lab 4 - RNA-seq downstream analysis</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/Lecture10_HiC.html"><span class="chapter-number">18</span> <span class="chapter-title">Lecture 10 - HiC processing</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day5/Lecture11_GO-GSEA.html"><span class="chapter-number">19</span> <span class="chapter-title">Lecture 11 - GO and GSEA analysis</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day5/Demo5_Bioc-resources.html"><span class="chapter-number">20</span> <span class="chapter-title">Demo 5 - Leveraging Bioconductor resources</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day5/Lab5_data-integration.html"><span class="chapter-number">21</span> <span class="chapter-title">Lab 5 - Multi-omics data integration</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">Epigenomics Data Analysis |<br /> J. Serizay</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-5d0d9e50bf708684c2c6e57b56ae9e8c">Day 2</span> <span class="hidden" data-render-id="quarto-breadcrumbs-c9a86e879356478bd3d02c6c0e0636f1"><span class="chapter-number">6</span> <span class="chapter-title">Lecture 4 - ATAC-seq processing and analyis</span></span></p> </div> <div id="quarto-meta-markdown" class="hidden"> <p><span class="hidden" data-render-id="quarto-metatitle">Epigenomics Data Analysis - <span class="chapter-number">6</span> <span class="chapter-title">Lecture 4 - ATAC-seq processing and analyis</span></span> <span class="hidden" data-render-id="quarto-twittercardtitle">Epigenomics Data Analysis - <span class="chapter-number">6</span> <span class="chapter-title">Lecture 4 - ATAC-seq processing and analyis</span></span> <span class="hidden" data-render-id="quarto-ogcardtitle">Epigenomics Data Analysis - <span class="chapter-number">6</span> <span class="chapter-title">Lecture 4 - ATAC-seq processing and analyis</span></span> <span class="hidden" data-render-id="quarto-metasitename">Epigenomics Data Analysis</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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