# Generated by roxygen2: do not edit by hand

export(AMARETTO_CreateModuleData)

export(AMARETTO_CreateRegulatorPrograms)

export(AMARETTO_Download)

export(AMARETTO_EvaluateTestSet)

export(AMARETTO_ExportResults)

export(AMARETTO_HTMLreport)

export(AMARETTO_Initialize)

export(AMARETTO_Preprocess)

export(AMARETTO_Run)

export(AMARETTO_VisualizeModule)

export(plot_run_history)

export(read_gct)

import(MultiAssayExperiment)

import(Rcpp, except = .DollarNames)

import(callr, except = run)

import(dplyr)

import(ggplot2)

import(grDevices)

import(graphics)

import(methods)

import(utils, except = prompt)

importFrom(BiocFileCache,BiocFileCache)

importFrom(BiocFileCache,bfcadd)

importFrom(BiocFileCache,bfcquery)

importFrom(ComplexHeatmap,Heatmap)

importFrom(ComplexHeatmap,HeatmapAnnotation)

importFrom(ComplexHeatmap,draw)

importFrom(DT,datatable)

importFrom(DT,formatRound)

importFrom(DT,formatSignif)

importFrom(DT,formatStyle)

importFrom(DT,styleColorBar)

importFrom(DT,styleInterval)

importFrom(Matrix,nnzero)

importFrom(MultiAssayExperiment,experiments)

importFrom(circlize,colorRamp2)

importFrom(circlize,rand_color)

importFrom(curatedTCGAData,curatedTCGAData)

importFrom(doParallel,registerDoParallel)

importFrom(dplyr,arrange)

importFrom(dplyr,case_when)

importFrom(dplyr,everything)

importFrom(dplyr,filter)

importFrom(dplyr,group_by)

importFrom(dplyr,left_join)

importFrom(dplyr,mutate)

importFrom(dplyr,rename)

importFrom(dplyr,select)

importFrom(dplyr,summarise)

importFrom(foreach,"%do%")

importFrom(foreach,"%dopar%")

importFrom(foreach,foreach)

importFrom(glmnet,cv.glmnet)

importFrom(graphics,lines)

importFrom(graphics,par)

importFrom(graphics,title)

importFrom(grid,gpar)

importFrom(grid,unit)

importFrom(gridExtra,grid.arrange)

importFrom(httr,GET)

importFrom(httr,stop_for_status)

importFrom(impute,impute.knn)

importFrom(knitr,knit_meta)

importFrom(limma,strsplit2)

importFrom(matrixStats,rowMads)

importFrom(matrixStats,rowVars)

importFrom(parallel,makeCluster)

importFrom(parallel,stopCluster)

importFrom(readr,write_tsv)

importFrom(reshape2,melt)

importFrom(rmarkdown,render)

importFrom(stats,aov)

importFrom(stats,coef)

importFrom(stats,cor)

importFrom(stats,density)

importFrom(stats,dist)

importFrom(stats,dnorm)

importFrom(stats,hclust)

importFrom(stats,kmeans)

importFrom(stats,lm)

importFrom(stats,na.omit)

importFrom(stats,p.adjust)

importFrom(stats,phyper)

importFrom(stats,prcomp)

importFrom(stats,qqline)

importFrom(stats,qqnorm)

importFrom(stats,qqplot)

importFrom(stats,rgamma)

importFrom(stats,sd)

importFrom(stats,var)

importFrom(tibble,column_to_rownames)

importFrom(tibble,rownames_to_column)

importFrom(utils,data)

importFrom(utils,install.packages)

importFrom(utils,read.csv)

importFrom(utils,read.delim)

importFrom(utils,untar)

importFrom(utils,write.table)

importFrom(utils,zip)