# Generated by roxygen2: do not edit by hand

S3method(gINTomics::residuals,DGEGLM)
export(create_multiassay)
export(dot_plotly)
export(extract_model_res)
export(plot_chr_distribution)
export(plot_heatmap)
export(plot_network)
export(plot_ridge)
export(plot_tf_distribution)
export(plot_venn)
export(plot_volcano)
export(run_cnv_integration)
export(run_genomic_enrich)
export(run_genomic_integration)
export(run_met_integration)
export(run_multiomics)
export(run_shiny)
export(run_tf_enrich)
export(run_tf_integration)
import(BiocParallel)
import(MultiAssayExperiment)
import(SummarizedExperiment)
importClassesFrom(edgeR,DGEGLM)
importFrom(AnnotationDbi,columns)
importFrom(AnnotationDbi,select)
importFrom(BiocGenerics,lapply)
importFrom(BiocGenerics,which.max)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpparam)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,ht_opt)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(DT,dataTableOutput)
importFrom(DT,datatable)
importFrom(DT,renderDataTable)
importFrom(GenomicFeatures,genes)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(InteractiveComplexHeatmap,InteractiveComplexHeatmapOutput)
importFrom(InteractiveComplexHeatmap,makeInteractiveComplexHeatmap)
importFrom(MASS,negative.binomial)
importFrom(OmnipathR,import_mirnatarget_interactions)
importFrom(OmnipathR,import_tf_mirna_interactions)
importFrom(OmnipathR,import_tf_target_interactions)
importFrom(RColorBrewer,brewer.pal)
importFrom(ReactomePA,enrichPathway)
importFrom(TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene)
importFrom(TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene)
importFrom(biomaRt,getBM)
importFrom(biomaRt,useMart)
importFrom(callr,r_bg)
importFrom(circlize,colorRamp2)
importFrom(clusterProfiler,enrichGO)
importFrom(clusterProfiler,enrichKEGG)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,desc)
importFrom(dplyr,filter)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate_all)
importFrom(dplyr,mutate_if)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,cpm)
importFrom(edgeR,estimateGLMCommonDisp)
importFrom(edgeR,estimateGLMTagwiseDisp)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(edgeR,topTags)
importFrom(ggplot2,aes)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,theme_void)
importFrom(ggridges,geom_density_ridges)
importFrom(ggridges,position_raincloud)
importFrom(ggridges,theme_ridges)
importFrom(ggtree,fortify)
importFrom(ggvenn,ggvenn)
importFrom(grDevices,colorRamp)
importFrom(grDevices,colorRampPalette)
importFrom(gtools,mixedsort)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,normalizeBetweenArrays)
importFrom(limma,topTable)
importFrom(methods,is)
importFrom(methods,new)
importFrom(org.Hs.eg.db,org.Hs.eg.db)
importFrom(org.Mm.eg.db,org.Mm.eg.db)
importFrom(plotly,add_markers)
importFrom(plotly,ggplotly)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(plotly,plotlyOutput)
importFrom(plotly,renderPlotly)
importFrom(plotly,subplot)
importFrom(plyr,rbind.fill)
importFrom(randomForest,importance)
importFrom(randomForest,randomForest)
importFrom(reshape2,melt)
importFrom(shiny,HTML)
importFrom(shiny,NS)
importFrom(shiny,a)
importFrom(shiny,actionButton)
importFrom(shiny,addResourcePath)
importFrom(shiny,bindEvent)
importFrom(shiny,callModule)
importFrom(shiny,checkboxInput)
importFrom(shiny,column)
importFrom(shiny,conditionalPanel)
importFrom(shiny,div)
importFrom(shiny,downloadButton)
importFrom(shiny,downloadHandler)
importFrom(shiny,fluidPage)
importFrom(shiny,fluidRow)
importFrom(shiny,htmlOutput)
importFrom(shiny,icon)
importFrom(shiny,img)
importFrom(shiny,inputPanel)
importFrom(shiny,invalidateLater)
importFrom(shiny,isolate)
importFrom(shiny,mainPanel)
importFrom(shiny,observe)
importFrom(shiny,onStop)
importFrom(shiny,plotOutput)
importFrom(shiny,radioButtons)
importFrom(shiny,reactive)
importFrom(shiny,renderPlot)
importFrom(shiny,renderText)
importFrom(shiny,renderUI)
importFrom(shiny,selectInput)
importFrom(shiny,shinyApp)
importFrom(shiny,sidebarLayout)
importFrom(shiny,sidebarPanel)
importFrom(shiny,sliderInput)
importFrom(shiny,span)
importFrom(shiny,tabPanel)
importFrom(shiny,tabsetPanel)
importFrom(shiny,tagList)
importFrom(shiny,tags)
importFrom(shiny,textOutput)
importFrom(shiny,uiOutput)
importFrom(shiny.gosling,add_multi_tracks)
importFrom(shiny.gosling,add_single_track)
importFrom(shiny.gosling,arrange_views)
importFrom(shiny.gosling,compose_view)
importFrom(shiny.gosling,export_pdf)
importFrom(shiny.gosling,export_png)
importFrom(shiny.gosling,gosling)
importFrom(shiny.gosling,goslingOutput)
importFrom(shiny.gosling,renderGosling)
importFrom(shiny.gosling,track_data_gr)
importFrom(shiny.gosling,use_gosling)
importFrom(shiny.gosling,visual_channel_color)
importFrom(shiny.gosling,visual_channel_stroke)
importFrom(shiny.gosling,visual_channel_stroke_width)
importFrom(shiny.gosling,visual_channel_tooltip)
importFrom(shiny.gosling,visual_channel_tooltips)
importFrom(shiny.gosling,visual_channel_x)
importFrom(shiny.gosling,visual_channel_y)
importFrom(shinydashboard,box)
importFrom(shinydashboard,dashboardBody)
importFrom(shinydashboard,dashboardHeader)
importFrom(shinydashboard,dashboardPage)
importFrom(shinydashboard,dashboardSidebar)
importFrom(shinydashboard,menuItem)
importFrom(shinydashboard,menuSubItem)
importFrom(shinydashboard,sidebarMenu)
importFrom(shinydashboard,tabItem)
importFrom(shinydashboard,tabItems)
importFrom(stats,IQR)
importFrom(stats,as.formula)
importFrom(stats,formula)
importFrom(stats,lm)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,poisson)
importFrom(stats,quantile)
importFrom(stats,relevel)
importFrom(stats,reorder)
importFrom(stats,residuals)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,terms)
importFrom(stringi,stri_replace_all_regex)
importFrom(stringr,str_wrap)
importFrom(utils,head)
importFrom(utils,write.csv)
importFrom(utils,write.table)
importFrom(visNetwork,renderVisNetwork)
importFrom(visNetwork,visEdges)
importFrom(visNetwork,visExport)
importFrom(visNetwork,visGroups)
importFrom(visNetwork,visHierarchicalLayout)
importFrom(visNetwork,visIgraphLayout)
importFrom(visNetwork,visLayout)
importFrom(visNetwork,visLegend)
importFrom(visNetwork,visNetwork)
importFrom(visNetwork,visNetworkOutput)
importFrom(visNetwork,visOptions)
