--- a
+++ b/NAMESPACE
@@ -0,0 +1,101 @@
+# 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)