Merge pull request #25 from GreenleafLab/dev_210304

update to discussions
GreenleafLab · Mar 4, 2021 · 937b13c · 937b13c
2 parents ed07b9c + 8699cbe
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diff --git a/docs/bookdown/index.html b/docs/bookdown/index.html
@@ -273,7 +273,7 @@ <h1><img src="images/ArchR_Logo_Integrated.png" alt="" width="200"></h1>
 <p>This website is a complete user’s guide to ArchR. We explain how to use ArchR by walking through examples of every analysis we could think of. We also include some more extensive documention on some of the more salient points of scATAC-seq analysis such as dimensionality reduction and clustering. All of the chapters will utilize the same downsampled dataset of hematopoietic cells <a href="https://www.ncbi.nlm.nih.gov/pubmed/31792411">Granja* et al. Nature Biotechnology 2019</a>. Each chapter will build on the previous so you should ideally start from the beginning and perform all analyses in sequence. <strong>Importantly, these tutorials assume that you are running ArchR locally</strong>.</p>
 <p>This walkthrough assumes that you have already successfully installed ArchR and all dependencies. If that is not the case, please <a href="https://www.archrproject.com/index.html">visit the home page</a> for installation instructions.</p>
 <p><i class="fa fa-search fa-2x"></i><span style="font-size:30px;font-weight:bold"> Cant find what you are looking for?</span></p>
-<p>There is a search feature that can be enabled using the magnifying glass in the navigation bar above which will help you find whatever it is you are looking for. If you dont find it in this book, or if you think the documentation on this website or in the function annotations is unclear, please <a href="https://github.com/GreenleafLab/ArchR/issues">submit an issue on Github</a> with the <strong>Documentation Request</strong> form and we will do our best to clarify. If none of these options help, <a href="mailto:archr.devs@gmail.com">send us an email</a> and we will do our best to respond in a timely fashion.</p>
+<p>There is a search feature that can be enabled using the magnifying glass in the navigation bar above which will help you find whatever it is you are looking for. If you dont find it in this book, or if you think the documentation on this website or in the function annotations is unclear, please <a href="https://github.com/GreenleafLab/ArchR/discussions">post to our Github Discussions forum</a> with the <strong>Q&A</strong> form and we will do our best to clarify. If none of these options help, <a href="mailto:archr.devs@gmail.com">send us an email</a> and we will do our best to respond in a timely fashion.</p>
 
 </div>
             </section>

diff --git a/docs/extras/ArchR_NatureGenetics.pdf b/docs/extras/ArchR_NatureGenetics.pdf
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   Articles/faq: faq.html
   Articles/tutorial: tutorial.html
-last_built: 2021-02-25T17:53Z
+last_built: 2021-03-04T15:38Z
 urls:
   reference: https://greenleaflab.github.io/ArchR_Website//reference
   article: https://greenleaflab.github.io/ArchR_Website//articles

diff --git a/index.md b/index.md
@@ -82,6 +82,6 @@ devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager
 ```
 If this does not fix your problem, please [report an issue on Github](https://github.com/GreenleafLab/ArchR/issues) with the __Bug Report__ form.
 
-If you have questions about ArchR usage, please refer to the [the searchable full user's manual](https://www.archrproject.com/bookdown/index.html), [the FAQ section](https://www.archrproject.com/articles/Articles/faq.html), and the [publication](https://greenleaf.stanford.edu/assets/pdf/). If you think the documentation on this website or in the function annotations is unclear, please [submit an issue on Github](https://github.com/GreenleafLab/ArchR/issues) with the __Documentation Request__ form. If there is a feature that you think is missing from ArchR _and you have already searched the user's manual_, [submit an issue on Github](https://github.com/GreenleafLab/ArchR/issues) with the __Feature Request__ form. If none of these options help, [send us an email](mailto:archr.devs@gmail.com). We will do our best to respond to questions that are not otherwise answered in the documentation.
+If you have questions about ArchR usage, please refer to the [the searchable full user's manual](https://www.archrproject.com/bookdown/index.html), [the FAQ section](https://www.archrproject.com/articles/Articles/faq.html), and the [publication](https://www.nature.com/articles/s41588-021-00790-6). If you think the documentation on this website or in the function annotations is unclear, please [post to the Github Discussions forum](https://github.com/GreenleafLab/ArchR/discussions) with the __Q&A__ form. If there is a feature that you think is missing from ArchR _and you have already searched the user's manual_, [post to the Github Discussions forum](https://github.com/GreenleafLab/ArchR/discussions) with the __Ideas__ form. If none of these options help, [send us an email](mailto:archr.devs@gmail.com). We will do our best to respond to questions that are not otherwise answered in the documentation.