R/GeneTonic-pkg.R
3df2ac39
 #' GeneTonic
 #'
16253045
 #' `GeneTonic` is a Bioconductor package that provides an interactive Shiny-based
2c89e2a2
 #' graphical user interface for streamlining the interpretation of RNA-seq data
fc8e87b6
 #'
 #' `GeneTonic` simplifies and optimizes the integration of all components of
bac708bd
 #' Differential Expression analysis, with functional enrichment analysis and the
2c89e2a2
 #' original expression quantifications.
fc8e87b6
 #' 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,
2c89e2a2
 #' code, and output coexist.
fc8e87b6
 #'
3df2ac39
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
5eab21da
 #'
8918a935
 #' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term
d1a1d486
 #' @importFrom backbone backbone.extract fdsm fixedrow sdsm
5426785a
 #' @importFrom bs4Dash bs4Card bs4DashBody bs4DashControlbar
 #' bs4DashFooter bs4DashNavbar bs4DashPage bs4DashSidebar
 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
 #' bs4SidebarMenuItem bs4TabItem bs4TabItems bs4ValueBox
 #' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox
3af53650
 #' bs4TabCard
ba212873
 #' @importFrom circlize colorRamp2
41c196cc
 #' @importFrom colorspace rainbow_hcl
db1e8aa8
 #' @importFrom colourpicker colourInput
8918a935
 #' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
20ce1cb7
 #' @importFrom ComplexUpset upset intersection_matrix intersection_size
8918a935
 #' @importFrom dendextend branches_attr_by_clusters set
 #' @importFrom DESeq2 vst counts estimateSizeFactors normalizationFactors sizeFactors
a6ba059e
 #' @importFrom dplyr arrange desc group_by mutate pull slice select "%>%"
4c6bc535
 #' @importFrom DT datatable dataTableOutput renderDataTable formatRound
 #' formatStyle JS
8918a935
 #' @importFrom dynamicTreeCut cutreeDynamic
9a039f19
 #' @importFrom expm "%^%"
597f500c
 #' @importFrom ggforce geom_sina
8918a935
 #' @import ggplot2
 #' @importFrom ggrepel geom_label_repel geom_text_repel
 #' @import GO.db
 #' @importFrom graphics par plot
0b927e85
 #' @importFrom grDevices colorRampPalette rgb col2rgb
8918a935
 #' @importFrom grid gpar
9dd9a108
 #' @importFrom igraph add_edges as_adjacency_matrix as_incidence_matrix degree
 #' delete.edges delete_vertices "%du%" E "E<-" graph.data.frame induced_subgraph
9a039f19
 #' make_full_graph permute.vertices strength V "V<-" vcount get.edgelist
8918a935
 #' @importFrom matrixStats rowSds
 #' @importFrom methods is
 #' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout add_trace
 #' @importFrom RColorBrewer brewer.pal
 #' @importFrom rintrojs introjs introjsUI
1a512e11
 #' @importFrom rlang .data
eb5cf1c6
 #' @importFrom rmarkdown render
8918a935
 #' @importFrom S4Vectors mcols
 #' @importFrom scales alpha muted
 #' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))
4a419aa1
 #' @importFrom shinyAce aceEditor
8918a935
 #' @importFrom shinycssloaders withSpinner
 #' @importFrom shinyWidgets dropdownButton tooltipOptions
0982f65b
 #' @importFrom stats var dist hclust as.dendrogram as.dist cmdscale median
 #' order.dendrogram runif na.omit
8918a935
 #' @import SummarizedExperiment
 #' @importFrom tidyr separate_rows pivot_longer
4a419aa1
 #' @importFrom tippy tippy
8a540d3c
 #' @importFrom tools file_ext file_path_sans_ext
748830b6
 #' @importFrom utils read.delim sessionInfo browseURL citation data write.table
0982f65b
 #' head
fc8e87b6
 #' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput
866b07c8
 #' visOptions
8918a935
 #' @importFrom viridis viridis
5eab21da
 #'
3df2ac39
 #' @name GeneTonic-pkg
 #' @docType package
 NULL