# Generated by roxygen2: do not edit by hand

export(compute_exome_coverage)
export(createOncoMatrix)
export(detectMAFGenome)
export(filterMAF)
export(filter_maf_chunked)
export(generateBurdenPlot)
export(generateMutationTypePlot)
export(generateOncoPlot)
export(generateOverlapPlot)
export(generateRibbonPlot)
export(generateTCGAComparePlot)
export(generateTiTvPlot)
export(generateVariantTable)
export(getMAFDashboard)
export(getMAFdataTCGA)
export(getTCGAClinicalAnnotation)
export(getTCGAClinicalColors)
import(bsplus)
import(canvasXpress)
import(circlize)
import(crosstalk)
import(flexdashboard)
import(ggplot2)
import(htmltools)
import(maftools)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,Legend)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,oncoPrint)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(DT,JS)
importFrom(DT,datatable)
importFrom(DT,formatStyle)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,reduce)
importFrom(IRanges,width)
importFrom(TCGAbiolinks,GDCquery_Maf)
importFrom(TCGAbiolinks,GDCquery_clinic)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,rbindlist)
importFrom(data.table,setDF)
importFrom(data.table,setDT)
importFrom(dplyr,"%>%")
importFrom(dplyr,all_of)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,pull)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(ensurer,ensure_that)
importFrom(ggbeeswarm,geom_quasirandom)
importFrom(grDevices,boxplot.stats)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,rainbow)
importFrom(graphics,strwidth)
importFrom(knitr,knit)
importFrom(pheatmap,pheatmap)
importFrom(plotly,ggplotly)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(plotly,plotly)
importFrom(plotly,subplot)
importFrom(readr,DataFrameCallback)
importFrom(readr,col_character)
importFrom(readr,cols)
importFrom(readr,read_tsv_chunked)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(rmarkdown,render)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,pairwise.t.test)
importFrom(stats,setNames)
importFrom(tibble,as_tibble)
importFrom(tidyr,pivot_longer)
importFrom(utils,count.fields)
importFrom(utils,globalVariables)
importFrom(utils,read.table)
importFrom(utils,write.table)
