# Generated by roxygen2: do not edit by hand

export(addZeroTime)
export(calcKinaseScore)
export(checkRatioMat)
export(clusterEnrich)
export(clusterTS)
export(enrichDifferential)
export(getDecouplerNetwork)
export(getRatioMatrix)
export(intensityBoxPlot)
export(makeSmartPhosDirectory)
export(medianNorm)
export(mscale)
export(normByFullProteome)
export(performCombinedNormalization)
export(performDifferentialExp)
export(plotAdjustmentResults)
export(plotHeatmap)
export(plotIntensity)
export(plotKinaseDE)
export(plotKinaseTimeSeries)
export(plotLogRatio)
export(plotMissing)
export(plotPCA)
export(plotTimeSeries)
export(plotVolcano)
export(preprocessPhos)
export(preprocessProteome)
export(readExperiment)
export(readExperimentDIA)
export(readPhosphoExperiment)
export(readPhosphoExperimentDIA)
export(readProteomeExperiment)
export(readProteomeExperimentDIA)
export(runFisher)
export(runGSEAforPhospho)
export(runPhosphoAdjustment)
export(runSmartPhos)
import(BiocParallel)
import(MultiAssayExperiment)
import(SummarizedExperiment)
import(ggplot2)
import(imputeLCMD)
importFrom(Biobase,rowMax)
importFrom(MsCoreUtils,impute_matrix)
importFrom(MultiAssayExperiment,assay)
importFrom(MultiAssayExperiment,assays)
importFrom(MultiAssayExperiment,colData)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(data.table,fread)
importFrom(data.table,rbindlist)
importFrom(decoupleR,check_corr)
importFrom(decoupleR,intersect_regulons)
importFrom(decoupleR,run_wmean)
importFrom(doParallel,registerDoParallel)
importFrom(doRNG,registerDoRNG)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,count)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,slice_max)
importFrom(dplyr,summarise)
importFrom(dplyr,tibble)
importFrom(dplyr,ungroup)
importFrom(e1071,cmeans)
importFrom(grDevices,colorRampPalette)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,removeBatchEffect)
importFrom(limma,topTable)
importFrom(magrittr,"%>%")
importFrom(matrixStats,colMedians)
importFrom(matrixStats,rowMads)
importFrom(missForest,missForest)
importFrom(parallel,makeCluster)
importFrom(parallel,setDefaultCluster)
importFrom(parallel,stopCluster)
importFrom(pheatmap,pheatmap)
importFrom(piano,GSAsummaryTable)
importFrom(piano,runGSA)
importFrom(proDA,proDA)
importFrom(proDA,test_diff)
importFrom(rlang,sym)
importFrom(splines,ns)
importFrom(stats,aggregate)
importFrom(stats,fisher.test)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,optim)
importFrom(stats,p.adjust)
importFrom(stats,reorder)
importFrom(stats,sd)
importFrom(stringr,str_ends)
importFrom(stringr,str_extract)
importFrom(stringr,str_split)
importFrom(tibble,as_tibble)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,separate)
importFrom(utils,combn)
importFrom(utils,data)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(vsn,justvsn)
