@@ -17,6 +17,7 @@ Imports:

     scales,

     RColorBrewer,

     grDevices,

+    graphics,

     S4Vectors,

     ggplot2,

     ggrepel,

@@ -31,17 +32,17 @@ Imports:

     DESeq2,

     ComplexHeatmap,

     grid,

-    pcaExplorer,

     methods,

     shinycssloaders,

     bs4Dash,

     shinyWidgets,

-    ggalluvial,

     viridis,

     dplyr,

     ggforce,

     rlang,

-    rmarkdown

+    rmarkdown,

+    dendextend,

+    dynamicTreeCut

 Suggests:

     knitr,

     BiocStyle,

@@ -31,26 +31,24 @@ export(overlap_coefficient)

 export(overlap_jaccard_index)

 export(shake_enrichResult)

 export(shake_topGOtableResult)

-import(DESeq2)

 import(GO.db)

 import(SummarizedExperiment)

-import(ggalluvial)

 import(ggplot2)

-import(igraph)

-import(pcaExplorer)

 import(shiny, except = c(renderDataTable, dataTableOutput))

-import(shinyWidgets)

-import(shinycssloaders)

-import(viridis)

-import(visNetwork)

 importFrom(AnnotationDbi,Definition)

 importFrom(AnnotationDbi,GOID)

+importFrom(AnnotationDbi,Ontology)

 importFrom(AnnotationDbi,Secondary)

 importFrom(AnnotationDbi,Synonym)

 importFrom(AnnotationDbi,Term)

 importFrom(ComplexHeatmap,Heatmap)

 importFrom(ComplexHeatmap,HeatmapAnnotation)

 importFrom(ComplexHeatmap,draw)

+importFrom(DESeq2,counts)

+importFrom(DESeq2,estimateSizeFactors)

+importFrom(DESeq2,normalizationFactors)

+importFrom(DESeq2,sizeFactors)

+importFrom(DESeq2,vst)

 importFrom(DT,dataTableOutput)

 importFrom(DT,datatable)

 importFrom(DT,renderDataTable)

@@ -75,15 +73,30 @@ importFrom(bs4Dash,bs4ValueBox)

 importFrom(bs4Dash,bs4ValueBoxOutput)

 importFrom(bs4Dash,renderbs4InfoBox)

 importFrom(bs4Dash,renderbs4ValueBox)

+importFrom(dendextend,branches_attr_by_clusters)

+importFrom(dendextend,set)

+importFrom(dplyr,"%>%")

 importFrom(dplyr,arrange)

 importFrom(dplyr,desc)

 importFrom(dplyr,group_by)

 importFrom(dplyr,mutate)

+importFrom(dplyr,pull)

+importFrom(dynamicTreeCut,cutreeDynamic)

 importFrom(ggforce,geom_sina)

 importFrom(ggrepel,geom_label_repel)

+importFrom(ggrepel,geom_text_repel)

 importFrom(grDevices,colorRampPalette)

 importFrom(grDevices,rgb)

+importFrom(graphics,par)

+importFrom(graphics,plot)

 importFrom(grid,gpar)

+importFrom(igraph,"E<-")

+importFrom(igraph,"V<-")

+importFrom(igraph,E)

+importFrom(igraph,V)

+importFrom(igraph,delete.edges)

+importFrom(igraph,graph.data.frame)

+importFrom(igraph,permute.vertices)

 importFrom(matrixStats,rowSds)

 importFrom(methods,is)

 importFrom(plotly,add_trace)

@@ -98,10 +111,26 @@ importFrom(rlang,.data)

 importFrom(rmarkdown,render)

 importFrom(scales,alpha)

 importFrom(scales,muted)

+importFrom(shinyWidgets,dropdownButton)

+importFrom(shinyWidgets,tooltipOptions)

+importFrom(shinycssloaders,withSpinner)

+importFrom(stats,as.dendrogram)

+importFrom(stats,as.dist)

+importFrom(stats,cmdscale)

 importFrom(stats,dist)

 importFrom(stats,hclust)

+importFrom(stats,median)

+importFrom(stats,order.dendrogram)

+importFrom(stats,runif)

 importFrom(stats,var)

 importFrom(tidyr,pivot_longer)

 importFrom(tidyr,separate_rows)

+importFrom(utils,browseURL)

+importFrom(utils,citation)

 importFrom(utils,read.delim)

 importFrom(utils,sessionInfo)

+importFrom(viridis,viridis)

+importFrom(visNetwork,renderVisNetwork)

+importFrom(visNetwork,visIgraph)

+importFrom(visNetwork,visNetworkOutput)

+importFrom(visNetwork,visOptions)

@@ -5,44 +5,47 @@

 #'

 #' @author Federico Marini \email{marinif@@uni-mainz.de}

 #'

-#' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))

-#' @importFrom DT dataTableOutput renderDataTable datatable

-#' @importFrom rintrojs introjs introjsUI

-#' @import igraph

-#' @import visNetwork

-#' @importFrom utils read.delim sessionInfo

-#' @importFrom grDevices colorRampPalette rgb

-#' @importFrom RColorBrewer brewer.pal

-#' @importFrom scales alpha muted

-#' @importFrom S4Vectors mcols

-#' @import ggplot2

-#' @importFrom ggrepel geom_label_repel

-#' @import GO.db

-#' @import DESeq2

-#' @importFrom AnnotationDbi Definition GOID Term Synonym Secondary

-#' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout add_trace

-#' @importFrom tidyr separate_rows pivot_longer

-#' @importFrom stats var dist hclust

-#' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw

-#' @importFrom grid gpar

-#' @importFrom matrixStats rowSds

-#' @import SummarizedExperiment

-#' @importFrom methods is

-#' @import pcaExplorer

-#' @import shinycssloaders

+#' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term

 #' @importFrom bs4Dash bs4Card bs4DashBody bs4DashControlbar

 #' bs4DashFooter bs4DashNavbar bs4DashPage bs4DashSidebar

 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu

 #' bs4SidebarMenuItem bs4TabItem bs4TabItems bs4ValueBox

 #' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox

 #' bs4TabPanel bs4TabCard

-#' @import shinyWidgets

-#' @import ggalluvial

-#' @import viridis

-#' @importFrom dplyr arrange desc group_by mutate

+#' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw

+#' @importFrom dendextend branches_attr_by_clusters set

+#' @importFrom DESeq2 vst counts estimateSizeFactors normalizationFactors sizeFactors

+#' @importFrom dplyr arrange desc group_by mutate pull "%>%"

+#' @importFrom DT datatable dataTableOutput renderDataTable

+#' @importFrom dynamicTreeCut cutreeDynamic

 #' @importFrom ggforce geom_sina

+#' @import ggplot2

+#' @importFrom ggrepel geom_label_repel geom_text_repel

+#' @import GO.db

+#' @importFrom graphics par plot

+#' @importFrom grDevices colorRampPalette rgb

+#' @importFrom grid gpar

+#' @importFrom igraph delete.edges E "E<-" graph.data.frame

+#' permute.vertices V "V<-"

+#' @importFrom matrixStats rowSds

+#' @importFrom methods is

+#' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout add_trace

+#' @importFrom RColorBrewer brewer.pal

+#' @importFrom rintrojs introjs introjsUI

 #' @importFrom rlang .data

 #' @importFrom rmarkdown render

+#' @importFrom S4Vectors mcols

+#' @importFrom scales alpha muted

+#' @importFrom stats var dist hclust as.dendrogram as.dist cmdscale median

+#' order.dendrogram runif

+#' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))

+#' @importFrom shinycssloaders withSpinner

+#' @importFrom shinyWidgets dropdownButton tooltipOptions

+#' @import SummarizedExperiment

+#' @importFrom tidyr separate_rows pivot_longer

+#' @importFrom utils read.delim sessionInfo browseURL citation

+#' @importFrom visNetwork renderVisNetwork visIgraph visNetworkOutput visOptions

+#' @importFrom viridis viridis

 #'

 #' @name GeneTonic-pkg

 #' @docType package