Updated version to match Bioconductor

campbio · Dec 28, 2021 · 3a89bf5 · 3a89bf5
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: celda
 Title: CEllular Latent Dirichlet Allocation
-Version: 1.9.3
+Version: 1.10.0
 Authors@R: c(person("Joshua", "Campbell", email = "[email protected]",
     role = c("aut", "cre")),
     person("Shiyi", "Yang", email="[email protected]", role = c("aut")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# celda v1.10.0 (2021-12-28)
+
+* Update to match Bioconductor release version
+
 # celda v1.9.3 (2021-10-04)
 
 * Fixed bug in checking background matrix with decontX

diff --git a/README.md b/README.md
@@ -18,12 +18,19 @@ if (!requireNamespace("BiocManager", quietly = TRUE))
 BiocManager::install("celda")
 ```
 
-To install the development version (R >= 3.6) of **celda** from GitHub using `devtools`:
+The latest stable version  of **celda** can be installed from GitHub using `devtools`:
+
 ```
 library(devtools)
 install_github("campbio/celda")
 ```
 
+The development version of **celda** can also be installed from GitHub using `devtools`:
+```
+library(devtools)
+install_github("campbio/celda@devel")
+```
+
 **NOTE** For MAC OSX users, `devtools::install_github()` requires installation of **libgit2.** This can be installed via homebrew:
 ```
 brew install libgit2

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CONDUCT.html b/docs/CONDUCT.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/articles/celda_pbmc3k.html b/docs/articles/articles/celda_pbmc3k.html
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_clusters-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_clusters-1.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_identities-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_identities-1.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-1.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-2.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-2.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/diffExp_plot-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/diffExp_plot-1.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/diffExp_plot-2.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/diffExp_plot-2.png
diff --git a/.../articles/articles/celda_pbmc3k_files/figure-html/module_split_perplexity-1.png b/.../articles/articles/celda_pbmc3k_files/figure-html/module_split_perplexity-1.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/module_split_rpc-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/module_split_rpc-1.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-1.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-2.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-2.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-3.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-3.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/violin-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/violin-1.png
diff --git a/docs/articles/articles/decontX_pbmc4k.html b/docs/articles/articles/decontX_pbmc4k.html
diff --git a/docs/articles/articles/installation.html b/docs/articles/articles/installation.html
diff --git a/docs/articles/celda.html b/docs/articles/celda.html
diff --git a/docs/articles/celda_files/figure-html/module_split_rpc-1.png b/docs/articles/celda_files/figure-html/module_split_rpc-1.png
diff --git a/docs/articles/celda_files/figure-html/plot_grid_search-1.png b/docs/articles/celda_files/figure-html/plot_grid_search-1.png
diff --git a/docs/articles/celda_files/figure-html/rpc_cell-1.png b/docs/articles/celda_files/figure-html/rpc_cell-1.png
diff --git a/docs/articles/celda_files/figure-html/rpc_cell-2.png b/docs/articles/celda_files/figure-html/rpc_cell-2.png
diff --git a/docs/articles/celda_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/celda_files/figure-html/unnamed-chunk-3-1.png
diff --git a/docs/articles/decontX.html b/docs/articles/decontX.html
diff --git a/docs/articles/decontX_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/decontX_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo ([email protected]) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 2.11.4
+pandoc: 2.9.2.1
 pkgdown: 1.6.1
 pkgdown_sha: ~
 articles:
@@ -7,5 +7,5 @@ articles:
   articles/installation: installation.html
   celda: celda.html
   decontX: decontX.html
-last_built: 2021-10-04T16:07Z
+last_built: 2021-12-28T19:10Z
 
diff --git a/docs/reference/appendCeldaList.html b/docs/reference/appendCeldaList.html
diff --git a/docs/reference/availableModels.html b/docs/reference/availableModels.html
diff --git a/docs/reference/bestLogLikelihood.html b/docs/reference/bestLogLikelihood.html
diff --git a/docs/reference/celda.html b/docs/reference/celda.html
diff --git a/docs/reference/celdaCGGridSearchRes.html b/docs/reference/celdaCGGridSearchRes.html
diff --git a/docs/reference/celdaCGMod.html b/docs/reference/celdaCGMod.html
diff --git a/docs/reference/celdaCGSim.html b/docs/reference/celdaCGSim.html