102 lines (100 with data), 2.8 kB

# 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)