#' GeneTonic
 #'

 #' `GeneTonic` is a Bioconductor package that provides an interactive Shiny-based

 #' graphical user interface for streamlining the interpretation of RNA-seq data

 #'
 #' `GeneTonic` simplifies and optimizes the integration of all components of

 #' Differential Expression analysis, with functional enrichment analysis and the

 #' original expression quantifications.

 #' It does so in a way that makes it easier to generate insightful observations
 #' and hypothesis - combining the benefits of interactivity and reproducibility,
 #' e.g. by capturing the features and gene sets of interest highlighted during
 #' the live session, and creating an HTML report as an artifact where text,

 #' code, and output coexist.

 #'

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

 #'

 #' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term

 #' @importFrom backbone backbone.extract fdsm fixedrow sdsm

 #' @importFrom bs4Dash bs4Card bs4DashBody bs4DashControlbar
 #' bs4DashFooter bs4DashNavbar bs4DashPage bs4DashSidebar
 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
 #' bs4SidebarMenuItem bs4TabItem bs4TabItems bs4ValueBox
 #' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox

 #' bs4TabCard

 #' @importFrom circlize colorRamp2

 #' @importFrom colorspace rainbow_hcl

 #' @importFrom colourpicker colourInput

 #' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw

 #' @importFrom ComplexUpset upset intersection_matrix intersection_size

 #' @importFrom dendextend branches_attr_by_clusters set
 #' @importFrom DESeq2 vst counts estimateSizeFactors normalizationFactors sizeFactors

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

 #' @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 as_adjacency_matrix as_incidence_matrix degree
 #' delete.edges delete_vertices "%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
 #' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))

 #' @importFrom shinyAce aceEditor

 #' @importFrom shinycssloaders withSpinner
 #' @importFrom shinyWidgets dropdownButton tooltipOptions

 #' @importFrom stats var dist hclust as.dendrogram as.dist cmdscale median
 #' order.dendrogram runif na.omit

 #' @import SummarizedExperiment
 #' @importFrom tidyr separate_rows pivot_longer

 #' @importFrom tippy tippy

 #' @importFrom tools file_ext file_path_sans_ext

 #' @importFrom utils read.delim sessionInfo browseURL citation data write.table

 #' head

 #' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput

 #' visOptions

 #' @importFrom viridis viridis

 #'

 #' @name GeneTonic-pkg
 #' @docType package
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