R/GeneTonic-pkg.R

In GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

#' GeneTonic
#'
#' `GeneTonic` is a Bioconductor package that provides an interactive Shiny-based
#'  graphical user interface for...
#'
#' @author Federico Marini \email{marinif@@uni-mainz.de}
#'
#' @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
#' @importFrom colorspace rainbow_hcl
#' @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 formatRound
#' formatStyle JS
#' @importFrom dynamicTreeCut cutreeDynamic
#' @importFrom expm "%^%"
#' @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 col2rgb
#' @importFrom grid gpar
#' @importFrom igraph add_edges delete.edges "%du%" E "E<-" graph.data.frame induced_subgraph
#' make_full_graph permute.vertices strength V "V<-" vcount get.edgelist
#' @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 tools file_ext file_path_sans_ext
#' @importFrom utils read.delim sessionInfo browseURL citation data write.table
#' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput 
#' visOptions
#' @importFrom viridis viridis
#'
#' @name GeneTonic-pkg
#' @docType package
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