Skip to content

Commit

Permalink
Browse files Browse the repository at this point in the history
… into main
  • Loading branch information
jhudsl-robot committed Dec 7, 2023
2 parents 9074ceb + c7c517c commit e19c76f
Show file tree
Hide file tree
Showing 61 changed files with 124 additions and 192 deletions.
3 changes: 3 additions & 0 deletions docs/01-intro.md
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,9 @@

![](resources/images/01-intro_files/figure-docx//1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY_gd422c5de97_0_0.png){width=100%}

This is a *living* course meaning it is constantly changing and being updated. The goal for this course is to be a "wikipedia" of omic data.
If you'd like to contribute, [you can file a pull request on GitHub](https://github.com/fhdsl/Choosing_Genomics_Tools) if you are comfortable with that sort of thing or email `[email protected]` to ask how to get started.

## Target Audience

The course is intended for students in the biomedical sciences and researchers who have been given data and don't know what to do with it or would like an overview of the different genomic data types that are out there.
Expand Down
18 changes: 9 additions & 9 deletions docs/10c-spatial-transcriptomics.md

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion docs/404.html
Original file line number Diff line number Diff line change
Expand Up @@ -480,7 +480,7 @@
<li class="divider"></li>
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
<a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<a href="https://hutchdatascience.org/"><img src="assets/big-dasl-stacked.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
<p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span> <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
</ul>
Expand Down
15 changes: 4 additions & 11 deletions docs/About.md
Original file line number Diff line number Diff line change
Expand Up @@ -11,24 +11,16 @@ 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, [Carrie Wright], [Claire Mills] - Whole Genome Sequencing, [Jacob Greene] - ChIP-seq |
|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 Directors|[Jeff Leek]|
|Content Consultants|[Carrie Wright], [Cliff Meyer] - ATAC-seq, [Frederick Tan]|
|Content Consultants|[Carrie Wright]<br> [Cliff Meyer] - ATAC-seq <br> [Frederick Tan]<br>|
|Acknowledgments||
|**Production**||
|Content Publisher|[Ira Gooding]|
|Content Publishing Reviewers|[Ira Gooding]|
|**Technical**||
|Course Publishing Engineer|[Candace Savonen]|
|Template Publishing Engineers|[Candace Savonen], [Carrie Wright]|
|Publishing Maintenance Engineer|[Candace Savonen]|
|Technical Publishing Stylists|[Carrie Wright], [Candace Savonen]|
|Package Developers ([ottrpal])[Candace Savonen], [John Muschelli], [Carrie Wright]|
|**Art and Design**||
|Illustrator| [Candace Savonen]|
|Figure Artist| [Candace Savonen] and [Claire Mills]|
|Videographer|[Candace Savonen]|
|Videography Editor| [Candace Savonen]|
|**Funding**||
|Funder|[National Cancer Institute (NCI)](https://www.cancer.gov/) UE5 CA254170|
|Funding Staff| [Sandy Ormbrek], [Shasta Nicholson] |
Expand All @@ -47,7 +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 2023-10-16
## date 2023-12-07
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
Expand Down Expand Up @@ -103,6 +95,7 @@ These credits are based on our [course contributors table guidelines](https://gi
[Frederick Tan]: https://bse.carnegiescience.edu/dr-frederick-tan
[Jacob Greene]: https://www.linkedin.com/in/jacob-greene-890aa318a/
[Jeff Leek]: https://jtleek.com/
[Oscar Ospina]: https://linkedin.com/in/oscareospina/
[John Muschelli]: https://johnmuschelli.com/
[Sandy Ormbrek]: https://hutchdatascience.org/ourteam/
[Shasta Nicholson]: https://hutchdatascience.org/ourteam/
Expand Down
Binary file modified docs/Choosing-Genomics-Tools.docx
Binary file not shown.
2 changes: 1 addition & 1 deletion docs/a-very-general-genomics-overview.html
Original file line number Diff line number Diff line change
Expand Up @@ -480,7 +480,7 @@
<li class="divider"></li>
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
<a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<a href="https://hutchdatascience.org/"><img src="assets/big-dasl-stacked.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
<p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span> <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
</ul>
Expand Down
50 changes: 9 additions & 41 deletions docs/about-the-authors.html
Original file line number Diff line number Diff line change
Expand Up @@ -480,7 +480,7 @@
<li class="divider"></li>
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
<a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<a href="https://hutchdatascience.org/"><img src="assets/big-dasl-stacked.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
<p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span> <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
</ul>
Expand Down Expand Up @@ -543,77 +543,45 @@ <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, <a href="https://carriewright11.github.io/">Carrie Wright</a>, <a href="https://www.linkedin.com/in/claire-mills-dds-50883553">Claire Mills</a> - Whole Genome Sequencing, <a href="https://www.linkedin.com/in/jacob-greene-890aa318a/">Jacob Greene</a> - ChIP-seq</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>
</tr>
<tr class="odd">
<td>Content Directors</td>
<td><a href="https://jtleek.com/">Jeff Leek</a></td>
</tr>
<tr class="even">
<td>Content Consultants</td>
<td><a href="https://carriewright11.github.io/">Carrie Wright</a>, <a href="https://ds.dfci.harvard.edu/our-people/clifford-meyer-phd/">Cliff Meyer</a> - ATAC-seq, <a href="https://bse.carnegiescience.edu/dr-frederick-tan">Frederick Tan</a></td>
<td><a href="https://carriewright11.github.io/">Carrie Wright</a><br> <a href="https://ds.dfci.harvard.edu/our-people/clifford-meyer-phd/">Cliff Meyer</a> - ATAC-seq <br> <a href="https://bse.carnegiescience.edu/dr-frederick-tan">Frederick Tan</a><br></td>
</tr>
<tr class="odd">
<td>Acknowledgments</td>
<td></td>
</tr>
<tr class="even">
<td><strong>Production</strong></td>
<td></td>
</tr>
<tr class="odd">
<td>Content Publisher</td>
<td><a href="https://publichealth.jhu.edu/faculty/4130/ira-gooding">Ira Gooding</a></td>
</tr>
<tr class="even">
<td>Content Publishing Reviewers</td>
<td><a href="https://publichealth.jhu.edu/faculty/4130/ira-gooding">Ira Gooding</a></td>
</tr>
<tr class="odd">
<td><strong>Technical</strong></td>
<td></td>
</tr>
<tr class="even">
<tr class="odd">
<td>Course Publishing Engineer</td>
<td><a href="https://www.cansavvy.com/">Candace Savonen</a></td>
</tr>
<tr class="odd">
<tr class="even">
<td>Template Publishing Engineers</td>
<td><a href="https://www.cansavvy.com/">Candace Savonen</a>, <a href="https://carriewright11.github.io/">Carrie Wright</a></td>
</tr>
<tr class="even">
<tr class="odd">
<td>Publishing Maintenance Engineer</td>
<td><a href="https://www.cansavvy.com/">Candace Savonen</a></td>
</tr>
<tr class="odd">
<tr class="even">
<td>Technical Publishing Stylists</td>
<td><a href="https://carriewright11.github.io/">Carrie Wright</a>, <a href="https://www.cansavvy.com/">Candace Savonen</a></td>
</tr>
<tr class="even">
<td>Package Developers (<a href="https://github.com/jhudsl/ottrpal">ottrpal</a>)<a href="https://www.cansavvy.com/">Candace Savonen</a>, <a href="https://johnmuschelli.com/">John Muschelli</a>, <a href="https://carriewright11.github.io/">Carrie Wright</a></td>
<td></td>
</tr>
<tr class="odd">
<td><strong>Art and Design</strong></td>
<td>Package Developers (<a href="https://github.com/jhudsl/ottrpal">ottrpal</a>)<a href="https://www.cansavvy.com/">Candace Savonen</a>, <a href="https://johnmuschelli.com/">John Muschelli</a>, <a href="https://carriewright11.github.io/">Carrie Wright</a></td>
<td></td>
</tr>
<tr class="even">
<td>Illustrator</td>
<td><a href="https://www.cansavvy.com/">Candace Savonen</a></td>
</tr>
<tr class="odd">
<td>Figure Artist</td>
<td><a href="https://www.cansavvy.com/">Candace Savonen</a> and <a href="https://www.linkedin.com/in/claire-mills-dds-50883553">Claire Mills</a></td>
</tr>
<tr class="even">
<td>Videographer</td>
<td><a href="https://www.cansavvy.com/">Candace Savonen</a></td>
</tr>
<tr class="odd">
<td>Videography Editor</td>
<td><a href="https://www.cansavvy.com/">Candace Savonen</a></td>
</tr>
<tr class="even">
<td><strong>Funding</strong></td>
<td></td>
</tr>
Expand All @@ -638,7 +606,7 @@ <h1>About the Authors</h1>
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2023-10-16
## date 2023-12-07
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
Expand Down
2 changes: 1 addition & 1 deletion docs/annotating-genomes.html
Original file line number Diff line number Diff line change
Expand Up @@ -480,7 +480,7 @@
<li class="divider"></li>
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
<a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<a href="https://hutchdatascience.org/"><img src="assets/big-dasl-stacked.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
<p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span> <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
</ul>
Expand Down
Binary file added docs/assets/big-dasl-stacked.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
2 changes: 1 addition & 1 deletion docs/atac-seq-1.html
Original file line number Diff line number Diff line change
Expand Up @@ -480,7 +480,7 @@
<li class="divider"></li>
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
<a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<a href="https://hutchdatascience.org/"><img src="assets/big-dasl-stacked.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
<p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span> <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
</ul>
Expand Down
2 changes: 1 addition & 1 deletion docs/bulk-rna-seq-1.html
Original file line number Diff line number Diff line change
Expand Up @@ -480,7 +480,7 @@
<li class="divider"></li>
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
<a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<a href="https://hutchdatascience.org/"><img src="assets/big-dasl-stacked.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
<p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span> <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
</ul>
Expand Down
2 changes: 1 addition & 1 deletion docs/chip-seq-1.html
Original file line number Diff line number Diff line change
Expand Up @@ -480,7 +480,7 @@
<li class="divider"></li>
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
<a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<a href="https://hutchdatascience.org/"><img src="assets/big-dasl-stacked.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
<p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span> <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
</ul>
Expand Down
2 changes: 1 addition & 1 deletion docs/chromatin-methods-overview.html
Original file line number Diff line number Diff line change
Expand Up @@ -480,7 +480,7 @@
<li class="divider"></li>
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
<a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<a href="https://hutchdatascience.org/"><img src="assets/big-dasl-stacked.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
<p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span> <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
</ul>
Expand Down
2 changes: 1 addition & 1 deletion docs/considerations-for-choosing-tools.html
Original file line number Diff line number Diff line change
Expand Up @@ -480,7 +480,7 @@
<li class="divider"></li>
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
<a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<a href="https://hutchdatascience.org/"><img src="assets/big-dasl-stacked.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
<p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
<p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span> <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
</ul>
Expand Down
Loading

0 comments on commit e19c76f

Please sign in to comment.