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fhdsl · Feb 7, 2024 · c58c6f0 · c58c6f0
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diff --git a/docs/11b-sc-ATAC-Seq.md b/docs/11b-sc-ATAC-Seq.md
@@ -9,10 +9,7 @@ This chapter is incomplete! If you wish to contribute, please [go to this form](
 
 ## Learning Objectives
 
-```{r, fig.alt = "Learning objectives This chapter will demonstrate how to:
-Understand the basics of single cell ATAC-Seq data collection and processing workflow Identify the next steps for your particular single cell ATAC-Seq data. Formulate questions to ask about your single cell ATAC-Seq data", out.width = "100%", echo = FALSE}
-ottrpal::include_slide("https://docs.google.com/presentation/d/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY/edit#slide=id.g227d7dd1e08_0_41")
-```
+![](resources/images/11b-sc-ATAC-Seq_files/figure-docx//1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_g227d7dd1e08_0_41.png){width=100%}
 
 ## What are the goals of scATAC-seq analysis?
 

diff --git a/docs/About.md b/docs/About.md
@@ -39,7 +39,7 @@ These credits are based on our [course contributors table guidelines](https://gi
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2024-01-31                  
+##  date     2024-02-07                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            

diff --git a/docs/Choosing-Genomics-Tools.docx b/docs/Choosing-Genomics-Tools.docx
diff --git a/docs/about-the-authors.html b/docs/about-the-authors.html
@@ -629,7 +629,7 @@ <h1>About the Authors</h1>
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2024-01-31                  
+##  date     2024-02-07                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            

diff --git a/docs/index.html b/docs/index.html
@@ -537,7 +537,7 @@ <h1>
 </div>
 <div id="header">
 <h1 class="title">Choosing Genomics Tools</h1>
-<p class="date"><em>January, 2024</em></p>
+<p class="date"><em>February, 2024</em></p>
 </div>
 <div id="about-this-course" class="section level1 unnumbered">
 <h1>About this Course</h1>

diff --git a/docs/index.md b/docs/index.md
@@ -1,6 +1,6 @@
 ---
 title: "Choosing Genomics Tools"
-date: "January, 2024"
+date: "February, 2024"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: [book.bib]

diff --git a/docs/no_toc/11b-sc-ATAC-Seq.md b/docs/no_toc/11b-sc-ATAC-Seq.md
@@ -9,10 +9,7 @@ This chapter is incomplete! If you wish to contribute, please [go to this form](
 
 ## Learning Objectives
 
-```{r, fig.alt = "Learning objectives This chapter will demonstrate how to:
-Understand the basics of single cell ATAC-Seq data collection and processing workflow Identify the next steps for your particular single cell ATAC-Seq data. Formulate questions to ask about your single cell ATAC-Seq data", out.width = "100%", echo = FALSE}
-ottrpal::include_slide("https://docs.google.com/presentation/d/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY/edit#slide=id.g227d7dd1e08_0_41")
-```
+<img src="resources/images/11b-sc-ATAC-Seq_files/figure-html//1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_g227d7dd1e08_0_41.png" title="Learning objectives This chapter will demonstrate how to: Understand the basics of single cell ATAC-Seq data collection and processing workflow Identify the next steps for your particular single cell ATAC-Seq data. Formulate questions to ask about your single cell ATAC-Seq data" alt="Learning objectives This chapter will demonstrate how to: Understand the basics of single cell ATAC-Seq data collection and processing workflow Identify the next steps for your particular single cell ATAC-Seq data. Formulate questions to ask about your single cell ATAC-Seq data" width="100%" />
 
 ## What are the goals of scATAC-seq analysis?
 

diff --git a/docs/no_toc/About.md b/docs/no_toc/About.md
@@ -39,7 +39,7 @@ These credits are based on our [course contributors table guidelines](https://gi
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2024-01-31                  
+##  date     2024-02-07                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            

diff --git a/docs/no_toc/about-the-authors.html b/docs/no_toc/about-the-authors.html
@@ -629,7 +629,7 @@ <h1>About the Authors</h1>
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2024-01-31                  
+##  date     2024-02-07                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            

diff --git a/docs/no_toc/index.html b/docs/no_toc/index.html
@@ -537,7 +537,7 @@ <h1>
 </div>
 <div id="header">
 <h1 class="title">Choosing Genomics Tools</h1>
-<p class="date"><em>January, 2024</em></p>
+<p class="date"><em>February, 2024</em></p>
 </div>
 <div id="about-this-course" class="section level1 unnumbered">
 <h1>About this Course</h1>

diff --git a/docs/no_toc/index.md b/docs/no_toc/index.md
@@ -1,6 +1,6 @@
 ---
 title: "Choosing Genomics Tools"
-date: "January, 2024"
+date: "February, 2024"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: [book.bib]

diff --git a/...s/figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_gd422c5de97_0_16.png b/...s/figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_gd422c5de97_0_16.png
diff --git a/.../figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_g227d7dd1e08_0_41.png b/.../figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_g227d7dd1e08_0_41.png
diff --git a/docs/no_toc/search_index.json b/docs/no_toc/search_index.json
diff --git a/docs/no_toc/single-cell-atac-seq-1.html b/docs/no_toc/single-cell-atac-seq-1.html
@@ -542,7 +542,7 @@ <h1><span class="header-section-number">Chapter 17</span> Single cell ATAC-Seq</
 </div>
 <div id="learning-objectives-15" class="section level2" number="17.1">
 <h2><span class="header-section-number">17.1</span> Learning Objectives</h2>
-<p><code>{r, fig.alt = "Learning objectives This chapter will demonstrate how to: Understand the basics of single cell ATAC-Seq data collection and processing workflow Identify the next steps for your particular single cell ATAC-Seq data. Formulate questions to ask about your single cell ATAC-Seq data", out.width = "100%", echo = FALSE} ottrpal::include_slide("https://docs.google.com/presentation/d/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY/edit#slide=id.g227d7dd1e08_0_41")</code></p>
+<p><img src="resources/images/11b-sc-ATAC-Seq_files/figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_g227d7dd1e08_0_41.png" title="Learning objectives This chapter will demonstrate how to: Understand the basics of single cell ATAC-Seq data collection and processing workflow Identify the next steps for your particular single cell ATAC-Seq data. Formulate questions to ask about your single cell ATAC-Seq data" alt="Learning objectives This chapter will demonstrate how to: Understand the basics of single cell ATAC-Seq data collection and processing workflow Identify the next steps for your particular single cell ATAC-Seq data. Formulate questions to ask about your single cell ATAC-Seq data" width="100%" /></p>
 </div>
 <div id="what-are-the-goals-of-scatac-seq-analysis" class="section level2" number="17.2">
 <h2><span class="header-section-number">17.2</span> What are the goals of scATAC-seq analysis?</h2>

diff --git a/...s/figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_gd422c5de97_0_16.png b/...s/figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_gd422c5de97_0_16.png
diff --git a/.../figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_g227d7dd1e08_0_41.png b/.../figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_g227d7dd1e08_0_41.png
diff --git a/docs/search_index.json b/docs/search_index.json
diff --git a/docs/single-cell-atac-seq-1.html b/docs/single-cell-atac-seq-1.html
@@ -542,7 +542,7 @@ <h1><span class="header-section-number">Chapter 17</span> Single cell ATAC-Seq</
 </div>
 <div id="learning-objectives-15" class="section level2" number="17.1">
 <h2><span class="header-section-number">17.1</span> Learning Objectives</h2>
-<p><code>{r, fig.alt = "Learning objectives This chapter will demonstrate how to: Understand the basics of single cell ATAC-Seq data collection and processing workflow Identify the next steps for your particular single cell ATAC-Seq data. Formulate questions to ask about your single cell ATAC-Seq data", out.width = "100%", echo = FALSE} ottrpal::include_slide("https://docs.google.com/presentation/d/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY/edit#slide=id.g227d7dd1e08_0_41")</code></p>
+<p><img src="resources/images/11b-sc-ATAC-Seq_files/figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_g227d7dd1e08_0_41.png" title="Learning objectives This chapter will demonstrate how to: Understand the basics of single cell ATAC-Seq data collection and processing workflow Identify the next steps for your particular single cell ATAC-Seq data. Formulate questions to ask about your single cell ATAC-Seq data" alt="Learning objectives This chapter will demonstrate how to: Understand the basics of single cell ATAC-Seq data collection and processing workflow Identify the next steps for your particular single cell ATAC-Seq data. Formulate questions to ask about your single cell ATAC-Seq data" width="100%" /></p>
 </div>
 <div id="what-are-the-goals-of-scatac-seq-analysis" class="section level2" number="17.2">
 <h2><span class="header-section-number">17.2</span> What are the goals of scATAC-seq analysis?</h2>