Merge pull request #23 from GreenleafLab/dev_210223

Dev 210223

Author: rcorces

README.md

@@ -3,4 +3,12 @@
 To build the website:
 
 1. Make sure you have the most up-to-date version of the `DESCRIPTION` file and the `.Rd` files created from ArchR when the package is build. The `DESCRIPTION` file should be copied into the main folder of this repository. The `.Rd` files contain the function documentation and should be copied into `/man/`.
-2. In the `DESCRIPTION` file, add the following tag "URL: https://www.ArchRProject.com"
+2. In the `DESCRIPTION` file, add the following tag "URL: https://www.ArchRProject.com"
+3. You must have pandoc installed.
+4. You must have the `pkgdown` R library installed.
+5. In R, from the main repository directory (containing the index.md file), run `build_site()`. This will create a lot of HTML files in the `/docs/` folder.
+
+
+To build the book:
+
+Once you've build the book, copy all of the HTML files and required figures etc. into the `/docs/bookdown/` folder

docs/extras/ArchR_Citation.ris

@@ -1,16 +1,18 @@
 TY  - JOUR
-T1  - ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis
-JF  - bioRxiv
-DO  - 10.1101/2020.04.28.066498
-SP  - 2020.04.28.066498
-AU  - Granja, Jeffrey M
+AU  - Granja, Jeffrey M.
 AU  - Corces, M. Ryan
-AU  - Pierce, Sarah E
+AU  - Pierce, Sarah E.
 AU  - Bagdatli, S. Tansu
 AU  - Choudhry, Hani
-AU  - Chang, Howard
-AU  - Greenleaf, William
-Y1  - 2020/01/01
-UR  - http://biorxiv.org/content/early/2020/04/29/2020.04.28.066498.abstract
-N2  - The advent of large-scale single-cell chromatin accessibility profiling has accelerated our ability to map gene regulatory landscapes, but has outpaced the development of robust, scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; www.ArchRProject.com) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses including doublet removal, single-cell clustering and cell type identification, robust peak set generation, cellular trajectory identification, DNA element to gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility, and multi-omic integration with scRNA-seq. Enabling the analysis of over 1.2 million single cells within 8 hours on a standard Unix laptop, ArchR is a comprehensive analytical suite for end-to-end analysis of single-cell chromatin accessibility data that will accelerate the understanding of gene regulation at the resolution of individual cells.Competing Interest StatementW.J.G. and H.Y.C. are consultants for 10x Genomics who has licensed IP associated with ATAC-seq. W.J.G. has additional affiliations with Guardant Health (consultant) and Protillion Biosciences (co-founder and consultant). H.Y.C. is a co-founder of Accent Therapeutics, Boundless Bio, and a consultant for Arsenal Biosciences and Spring Discovery.
+AU  - Chang, Howard Y.
+AU  - Greenleaf, William J.
+PY  - 2021
+DA  - 2021/02/25
+TI  - ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
+JO  - Nature Genetics
+AB  - The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; https://www.archrproject.com/) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses, including doublet removal, single-cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing (scRNA-seq). Enabling the analysis of over 1.2 million single cells within 8 h on a standard Unix laptop, ArchR is a comprehensive software suite for end-to-end analysis of single-cell chromatin accessibility that will accelerate the understanding of gene regulation at the resolution of individual cells.
+SN  - 1546-1718
+UR  - https://doi.org/10.1038/s41588-021-00790-6
+DO  - 10.1038/s41588-021-00790-6
+ID  - Granja2021
 ER  - 

docs/index.html

@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   Articles/faq: faq.html
   Articles/tutorial: tutorial.html
-last_built: 2021-02-23T20:18Z
+last_built: 2021-02-25T17:53Z
 urls:
   reference: https://greenleaflab.github.io/ArchR_Website//reference
   article: https://greenleaflab.github.io/ArchR_Website//articles

docs/pkgdown.yml

@@ -4,7 +4,7 @@
 
 ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data. ArchR provides the most extensive suite of scATAC-seq analysis tools of any software available. Additionally, ArchR excels in both speed and resource usage, making it possible to analyze 1 million cells in 8 hours on a MacBook Pro laptop.
 
-To get started, we recommend running through [the brief ArchR tutorial](articles/Articles/tutorial.html). For a detailed description of all of the features of ArchR applied to a test dataset of hematopoietic cells, please see the searchable [full manual](bookdown/index.html). If you havent already done so, we also recommend reading [the publication](https://www.biorxiv.org/content/10.1101/2020.04.28.066498v1) to get a better idea of what ArchR can do.
+To get started, we recommend running through [the brief ArchR tutorial](articles/Articles/tutorial.html). For a detailed description of all of the features of ArchR applied to a test dataset of hematopoietic cells, please see the searchable [full manual](bookdown/index.html). If you havent already done so, we also recommend reading [the publication](https://www.nature.com/articles/s41588-021-00790-6) to get a better idea of what ArchR can do.
 
 <hr>
 
@@ -66,14 +66,15 @@ __If you have installed R through Conda__, we have had reports of compile errors
 
 # How to cite ArchR?
 
-Granja JM et al., An integrative and scalable software package for single-cell chromatin accessibility analysis. bioRxiv (2020)
+ArchR is published in Nature Genetics! You can find the publication [here](https://www.nature.com/articles/s41588-021-00790-6).
+Granja JM et al., ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nature Genetics (2021)
 [Download an RIS-format citation file here](extras/ArchR_Citation.ris).
 
 Looking for scripts related to the publication? Check out the [GitHub page for the publication](https://github.com/GreenleafLab/ArchR_2020).
 
 # Issues using ArchR?
 
-ArchR is currently in __beta__. We expect there to be bumps in the road. If you think you have found a bug, please first install the latest version of ArchR via
+ArchR is still in active development. We expect there to be bumps in the road. If you think you have found a bug, please first install the latest version of ArchR via
 ```{r}
 devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())
 ```