corceslab
diff --git a/Diff for: ‎DESCRIPTION
+3-1 b/Diff for: ‎DESCRIPTION
+3-1
diff --git a/Diff for: ‎README.md
+4-7 b/Diff for: ‎README.md
+4-7
diff --git a/Diff for: ‎docs/404.html
+1-1 b/Diff for: ‎docs/404.html
+1-1
diff --git a/Diff for: ‎docs/LICENSE-text.html
+1-1 b/Diff for: ‎docs/LICENSE-text.html
+1-1
diff --git a/Diff for: ‎docs/LICENSE.html
+1-1 b/Diff for: ‎docs/LICENSE.html
+1-1
diff --git a/Diff for: ‎docs/articles/CHOIR.html
+55-51 b/Diff for: ‎docs/articles/CHOIR.html
+55-51
diff --git a/Diff for: ‎docs/articles/index.html
+1-1 b/Diff for: ‎docs/articles/index.html
+1-1
diff --git a/Diff for: ‎docs/authors.html
+3-3 b/Diff for: ‎docs/authors.html
+3-3
diff --git a/Diff for: ‎docs/favicon-16x16.png
1.08 KB b/Diff for: ‎docs/favicon-16x16.png
1.08 KB
diff --git a/Diff for: ‎docs/favicon-32x32.png
1.45 KB b/Diff for: ‎docs/favicon-32x32.png
1.45 KB
diff --git a/Diff for: ‎docs/favicon.ico
14.7 KB b/Diff for: ‎docs/favicon.ico
14.7 KB
diff --git a/Diff for: ‎docs/favicon.png
77.6 KB b/Diff for: ‎docs/favicon.png
77.6 KB
diff --git a/Diff for: ‎docs/index.html
+8-13 b/Diff for: ‎docs/index.html
+8-13
diff --git a/Diff for: ‎docs/news/index.html
+87 b/Diff for: ‎docs/news/index.html
+87
diff --git a/Diff for: ‎docs/pkgdown.yml
+1-1 b/Diff for: ‎docs/pkgdown.yml
+1-1
@@ -4,7 +4,7 @@ Version: 0.1.0
 Authors@R: 
 	person("Cathrine", "Petersen", , "[email protected]", role = c("aut", "cre"), 
 		comment = c(ORCID = "0000-0002-5821-9828"))
-Description: CHOIR is a clustering algorithm for single-cell sequencing data. CHOIR applies a framework of permutation tests and random forest classifiers across a hierarchical clustering tree to statistically determine which clusters represent distinct populations.
+Description: CHOIR is a clustering algorithm for single-cell sequencing data. CHOIR applies a framework of permutation tests and random forest classifiers across a hierarchical clustering tree to statistically identify clusters that represent distinct populations.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
@@ -25,10 +25,12 @@ Imports:
     bluster,
     dplyr,
     ggplot2,
+    ggtree,
     harmony,
     magrittr,
     Matrix,
     methods,
+    mrtree,
     plyr,
     progress,
     ranger,
 
@@ -1,15 +1,12 @@
-# CHOIR
-
+<br>
 <a href ="https://www.CHOIRclustering.com"><img src="man/figures/CHOIR_logo.png" width="200px" align="right" />
 
 <!-- badges: start -->
 <!-- badges: end -->
 
-------
-
-CHOIR (**c**lustering **h**ierachy **o**ptimization by **i**terative **r**andom forests) is a clustering algorithm for single-cell sequencing data. CHOIR applies a framework of permutation tests and random forest classifiers across a hierarchical clustering tree to statistically determine which clusters represent distinct populations.
+**CHOIR** (**c**lustering **h**ierachy **o**ptimization by **i**terative **r**andom forests) is a clustering algorithm for single-cell sequencing data. CHOIR applies a framework of permutation tests and random forest classifiers across a hierarchical clustering tree to statistically identify clusters that represent distinct populations.
 
-------
+<br>
 
 ## Installation
 
@@ -20,7 +17,7 @@ remotes::install_github("corceslab/CHOIR", ref="main", repos = BiocManager::repo
 
 ## Usage
 
-Please follow the Quick Tutorial at [CHOIRclustering.com](https://www.CHOIRclustering.com). Alternately, install the package with `build_vignettes = TRUE`, as follows:
+Please follow the [vignette](https://www.choirclustering.com/articles/CHOIR.html). Alternately, install the package with `build_vignettes = TRUE`, as follows:
 ``` r
 remotes::install_github("corceslab/CHOIR", ref="main", repos = BiocManager::repositories(), upgrade = "never", build_vignettes = TRUE)
 ```
 
@@ -3,5 +3,5 @@ pkgdown: 2.0.4
 pkgdown_sha: ~
 articles:
   CHOIR: CHOIR.html
-last_built: 2023-10-20T04:09Z
+last_built: 2023-10-20T20:08Z