Devel

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: singleCellTK
 Type: Package
 Title: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
-Version: 2.15.2
+Version: 2.16.1
 Authors@R: c(person(given="Yichen", family="Wang", email="wangych@bu.edu", role=c("aut"),
                     comment = c(ORCID = "0000-0003-4347-5199")),
              person(given="Irzam", family="Sarfraz", email="isarfraz@bu.edu", role=c("aut"),

LICENSE

@@ -1,21 +1,2 @@
 YEAR: 2016
-COPYRIGHT HOLDER: David Jenkins and W. Evan Johnson
-
-The MIT License (MIT) (http://opensource.org/licenses/MIT)
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of
-this software and associated documentation files (the "Software"), to deal in
-the Software without restriction, including without limitation the rights to
-use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
-the Software, and to permit persons to whom the Software is furnished to do so,
-subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
-FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
-COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
-IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+COPYRIGHT HOLDER: David Jenkins, W. Evan Johnson, and Joshua D. Campbell

NEWS.md

@@ -1,7 +1,17 @@
+Changes in Version 2.16.1 (2024-02-12)
+================================================================================
+* Fixed decontX/soupX webapp error
+* Fixed error in reportCellQC 
+* Fixed additional bugs with Seurat V5 integration
+
+Changes in Version 2.16.0 (2024-10-29)
+================================================================================
+* Updated version to match Bioconductor 3.20
+
 Changes in Version 2.14.0 (2024-05-03)
 ================================================================================
 * Updated version to match Bioconductor 3.19
-* Update runGSVA fucntion to work with newer GSVA package
+* Update runGSVA function to work with newer GSVA package
 
 Changes in Version 2.12.2 (2024-01-28)
 ================================================================================

R/plotSCEHeatmap.R

@@ -290,7 +290,7 @@ plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,
    #colData(SCE) <- colData(SCE)[,c(aggregateCol),drop=FALSE] ##change
 
     temp_df<-as.data.frame(colData(SCE)[,c(aggregateCol),drop=FALSE]) %>% 
-      unite("new_colnames",1:ncol(.data),sep = "_",remove = FALSE) %>% 
+      unite("new_colnames",dplyr::everything(),sep = "_",remove = FALSE) %>% 
       remove_rownames() %>% 
     #  mutate(aggregated_column = new_colnames) %>%
     #  dplyr::select(new_colnames, aggregated_column) %>%

R/seuratFunctions.R

@@ -1117,7 +1117,7 @@ runSeuratUMAP <- function(inSCE,
 #' other libraries. Default \code{NULL}.
 #' @param interactive Logical value indicating if the returned object should
 #'  be an interactive plotly object if \code{TRUE} or a ggplot object if
-#'  set to \code{FALSE}. Default is \code{TRUE}.
+#'  set to \code{FALSE}. Default is \code{FALSE}.
 #' @examples
 #' data(scExample, package = "singleCellTK")
 #' \dontrun{
@@ -1134,7 +1134,7 @@ plotSeuratElbow <- function(inSCE,
                             reduction = "pca",
                             ndims = 20,
                             externalReduction = NULL,
-                            interactive = TRUE) {
+                            interactive = FALSE) {
   seuratObject <- convertSCEToSeurat(inSCE)
   if (!is.null(externalReduction)) {
     seuratObject@reductions <- list(pca = externalReduction)