Merge branch 'main' of https://github.com/fhdsl/Choosing_Genomics_Tools…

… into main
fhdsl · Jan 31, 2024 · 6a6e4a2 · 6a6e4a2
2 parents 3fb5e63 + c45f5ed
commit 6a6e4a2
Show file tree

Hide file tree

Showing 57 changed files with 6 additions and 198 deletions.
diff --git a/docs/no_toc/02-genomics_overview.md b/docs/no_toc/02-genomics_overview.md
@@ -1,6 +1,5 @@
 
 
-
 # A Very General Genomics Overview
 
 ## Learning Objectives

diff --git a/docs/no_toc/About.md b/docs/no_toc/About.md
@@ -11,7 +11,7 @@ These credits are based on our [course contributors table guidelines](https://gi
 |**Pedagogy**||
 |Lead Content Instructor(s)|[Candace Savonen]|
 |Lecturer(s)|[Candace Savonen]|
-|Content Contributor(s)| [Cailin Jordan] - sc-ATAC-Seq <br> [Carrie Wright] <br> [Claire Mills] - Whole Genome Sequencing<br> [Jacob Greene] - ChIP-seq <br> [Oscar Ospina] - Spatial transcriptomics|
+|Content Contributor(s)| [Cailin Jordan] - sc-ATAC-Seq <br> [Carrie Wright] <br> [Claire Mills] - Whole Genome Sequencing<br> [Jacob Greene] - ChIP-seq <br> [Oscar Ospina] - Spatial transcriptomics <br> [Ye Zheng] - CUTRUN/CUTTag|
 |Content Directors|[Jeff Leek]|
 |Content Consultants|[Carrie Wright]<br> [Cliff Meyer] - ATAC-seq <br> [Frederick Tan]<br>|
 |Acknowledgments||
@@ -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     2024-01-24                  
+##  date     2024-01-31                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            
@@ -113,7 +113,7 @@ These credits are based on our [course contributors table guidelines](https://gi
 [John Muschelli]: https://johnmuschelli.com/
 [Sandy Ormbrek]: https://hutchdatascience.org/ourteam/
 [Shasta Nicholson]: https://hutchdatascience.org/ourteam/
-
+[Ye Zheng]: https://yezhengstat.github.io/
 <!-- Links -->
 
 [ottrpal]: https://github.com/jhudsl/ottrpal
diff --git a/docs/no_toc/about-the-authors.html b/docs/no_toc/about-the-authors.html
@@ -566,7 +566,7 @@ <h1>About the Authors</h1>
 </tr>
 <tr class="even">
 <td>Content Contributor(s)</td>
-<td><a href="https://www.linkedin.com/in/cailin-jordan-3297b7199/">Cailin Jordan</a> - sc-ATAC-Seq <br> <a href="https://carriewright11.github.io/">Carrie Wright</a> <br> <a href="https://www.linkedin.com/in/claire-mills-dds-50883553">Claire Mills</a> - Whole Genome Sequencing<br> <a href="https://www.linkedin.com/in/jacob-greene-890aa318a/">Jacob Greene</a> - ChIP-seq <br> <a href="https://linkedin.com/in/oscareospina/">Oscar Ospina</a> - Spatial transcriptomics</td>
+<td><a href="https://www.linkedin.com/in/cailin-jordan-3297b7199/">Cailin Jordan</a> - sc-ATAC-Seq <br> <a href="https://carriewright11.github.io/">Carrie Wright</a> <br> <a href="https://www.linkedin.com/in/claire-mills-dds-50883553">Claire Mills</a> - Whole Genome Sequencing<br> <a href="https://www.linkedin.com/in/jacob-greene-890aa318a/">Jacob Greene</a> - ChIP-seq <br> <a href="https://linkedin.com/in/oscareospina/">Oscar Ospina</a> - Spatial transcriptomics <br> <a href="https://yezhengstat.github.io/">Ye Zheng</a> - CUTRUN/CUTTag</td>
 </tr>
 <tr class="odd">
 <td>Content Directors</td>
@@ -629,7 +629,7 @@ <h1>About the Authors</h1>
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2024-01-24                  
+##  date     2024-01-31                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            

diff --git a/...s/figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_g144bc8d6a68_0_7.png b/...s/figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_g144bc8d6a68_0_7.png
diff --git a/.../figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_g144bc8d6a68_0_12.png b/.../figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_g144bc8d6a68_0_12.png
diff --git a/.../figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_g2a3974d9533_0_10.png b/.../figure-html/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_g2a3974d9533_0_10.png
diff --git a/docs/no_toc/search_index.json b/docs/no_toc/search_index.json
diff --git a/manuscript/1-Introduction.md b/manuscript/1-Introduction.md
diff --git a/manuscript/10-Whole-Genome-or-Exome-Sequencing.md b/manuscript/10-Whole-Genome-or-Exome-Sequencing.md
diff --git a/manuscript/11-RNA-Methods-Overview.md b/manuscript/11-RNA-Methods-Overview.md
diff --git a/manuscript/12-Bulk-RNA-seq.md b/manuscript/12-Bulk-RNA-seq.md
diff --git a/manuscript/13-Single-cell-RNA-seq.md b/manuscript/13-Single-cell-RNA-seq.md
diff --git a/manuscript/14-Spatial-transcriptomics.md b/manuscript/14-Spatial-transcriptomics.md
diff --git a/manuscript/15-Chromatin-Methods-Overview.md b/manuscript/15-Chromatin-Methods-Overview.md
diff --git a/manuscript/16-ATAC-Seq.md b/manuscript/16-ATAC-Seq.md
diff --git a/manuscript/17-Single-cell-ATAC-Seq.md b/manuscript/17-Single-cell-ATAC-Seq.md
diff --git a/manuscript/18-ChIP-Seq.md b/manuscript/18-ChIP-Seq.md
diff --git a/manuscript/19-DNA-Methylation-Sequencing.md b/manuscript/19-DNA-Methylation-Sequencing.md
diff --git a/manuscript/2-A-Very-General-Genomics-Overview.md b/manuscript/2-A-Very-General-Genomics-Overview.md
diff --git a/manuscript/20-ITCR--omic-Tool-Glossary.md b/manuscript/20-ITCR--omic-Tool-Glossary.md
diff --git a/manuscript/3-Guidelines-for-Good-Metadata.md b/manuscript/3-Guidelines-for-Good-Metadata.md
diff --git a/manuscript/3-What-are-Metadata?.md b/manuscript/3-What-are-Metadata?.md
diff --git a/manuscript/4-Considerations-for-choosing-tools.md b/manuscript/4-Considerations-for-choosing-tools.md
diff --git a/manuscript/5-General-Data-Analysis-Tools.md b/manuscript/5-General-Data-Analysis-Tools.md
diff --git a/manuscript/6-Sequencing-Data.md b/manuscript/6-Sequencing-Data.md
diff --git a/manuscript/7-Microarray-Data.md b/manuscript/7-Microarray-Data.md
diff --git a/manuscript/8-Annotating-Genomes.md b/manuscript/8-Annotating-Genomes.md
diff --git a/manuscript/9-DNA-Methods-Overview.md b/manuscript/9-DNA-Methods-Overview.md
diff --git a/manuscript/About-the-Authors.md b/manuscript/About-the-Authors.md
diff --git a/manuscript/About-this-Course.md b/manuscript/About-this-Course.md
diff --git a/manuscript/Book.txt b/manuscript/Book.txt
diff --git a/manuscript/References.md b/manuscript/References.md
diff --git a/manuscript/resources/chapt_screen_images/a-very-general-genomics-overview.png b/manuscript/resources/chapt_screen_images/a-very-general-genomics-overview.png
diff --git a/manuscript/resources/chapt_screen_images/about-the-authors.png b/manuscript/resources/chapt_screen_images/about-the-authors.png
diff --git a/manuscript/resources/chapt_screen_images/annotating-genomes.png b/manuscript/resources/chapt_screen_images/annotating-genomes.png
diff --git a/manuscript/resources/chapt_screen_images/atac-seq-1.png b/manuscript/resources/chapt_screen_images/atac-seq-1.png
diff --git a/manuscript/resources/chapt_screen_images/bulk-rna-seq-1.png b/manuscript/resources/chapt_screen_images/bulk-rna-seq-1.png
diff --git a/manuscript/resources/chapt_screen_images/chip-seq-1.png b/manuscript/resources/chapt_screen_images/chip-seq-1.png
diff --git a/manuscript/resources/chapt_screen_images/chromatin-methods-overview.png b/manuscript/resources/chapt_screen_images/chromatin-methods-overview.png
diff --git a/manuscript/resources/chapt_screen_images/considerations-for-choosing-tools.png b/manuscript/resources/chapt_screen_images/considerations-for-choosing-tools.png
diff --git a/manuscript/resources/chapt_screen_images/dna-methods-overview.png b/manuscript/resources/chapt_screen_images/dna-methods-overview.png
diff --git a/manuscript/resources/chapt_screen_images/dna-methylation-sequencing.png b/manuscript/resources/chapt_screen_images/dna-methylation-sequencing.png
diff --git a/manuscript/resources/chapt_screen_images/general-data-analysis-tools.png b/manuscript/resources/chapt_screen_images/general-data-analysis-tools.png
diff --git a/manuscript/resources/chapt_screen_images/guidelines-for-good-metadata.png b/manuscript/resources/chapt_screen_images/guidelines-for-good-metadata.png
diff --git a/manuscript/resources/chapt_screen_images/index.png b/manuscript/resources/chapt_screen_images/index.png
diff --git a/manuscript/resources/chapt_screen_images/introduction.png b/manuscript/resources/chapt_screen_images/introduction.png
diff --git a/manuscript/resources/chapt_screen_images/itcr--omic-tool-glossary.png b/manuscript/resources/chapt_screen_images/itcr--omic-tool-glossary.png
diff --git a/manuscript/resources/chapt_screen_images/microarray-data.png b/manuscript/resources/chapt_screen_images/microarray-data.png
diff --git a/manuscript/resources/chapt_screen_images/references.png b/manuscript/resources/chapt_screen_images/references.png
diff --git a/manuscript/resources/chapt_screen_images/rna-methods-overview.png b/manuscript/resources/chapt_screen_images/rna-methods-overview.png
diff --git a/manuscript/resources/chapt_screen_images/sequencing-data.png b/manuscript/resources/chapt_screen_images/sequencing-data.png
diff --git a/manuscript/resources/chapt_screen_images/single-cell-atac-seq-1.png b/manuscript/resources/chapt_screen_images/single-cell-atac-seq-1.png
diff --git a/manuscript/resources/chapt_screen_images/single-cell-rna-seq.png b/manuscript/resources/chapt_screen_images/single-cell-rna-seq.png
diff --git a/manuscript/resources/chapt_screen_images/spatial-transcriptomics-1.png b/manuscript/resources/chapt_screen_images/spatial-transcriptomics-1.png
diff --git a/manuscript/resources/chapt_screen_images/whole-genome-or-exome-sequencing.png b/manuscript/resources/chapt_screen_images/whole-genome-or-exome-sequencing.png
diff --git a/resources/chapt_screen_images/about-the-authors.png b/resources/chapt_screen_images/about-the-authors.png
diff --git a/resources/chapt_screen_images/sequencing-data.png b/resources/chapt_screen_images/sequencing-data.png
Original file line number	Diff line number	Diff line change
		@@ -1,6 +1,5 @@



		# A Very General Genomics Overview

		## Learning Objectives
Expand Down