export(analyzeTPPCCR)
export(analyzeTPPTR)
export(analyze2DTPP)
export(tppDefaultTheme)
export(tppExport)
export(tppQCPlotsCorrelateExperiments)
export(tppccrCurveFit)
export(tppccrImport)
export(tppccrNormalize)
export(tppccrNormalizeToReference)
export(tppccrPlotCurves)
export(tppccrResultTable)
export(tppccrTransform)
export(tpptrAnalyzeMeltingCurves)
export(tpptrCurveFit)
export(tpptrDefaultNormReqs)
export(tpptrImport)
export(tpptrNormalize)
export(tpptrSplineFitAndTest)
export(tpptrFitSplines)
export(tpptrPlotSplines)
export(tpptrFTest)
export(tpptrTidyUpESets)
export(tpp2dAddAdditionalInfo) # export necessary? specialized function -> how often stabilized?
export(tpp2dEvalConfigTable) # DEPRECATED
export(tpp2dCalcFractAbundance) # export necessary? specialized function
export(tpp2dComputeFoldChanges)
export(tpp2dCreateCCRConfigFile) # DEPRECATED
export(tpp2dCreateDRplots)
export(tpp2dCreateReport)
export(tpp2dCreateTPPTRreference)  # initialize object
export(tpp2dCurveFit)
export(tpp2dExport)
export(tpp2dExportPlots)
export(tpp2dImport)
export(tpp2dMerge2dRef) # export necessary, or should it be made part of tpp2dExport? specialized function, adds reference summary to 2D output
export(tpp2dNormalize)
export(tpp2dPlotCCRAllCurves)
export(tpp2dPlotCCRGoodCurves)
export(tpp2dPlotCCRSingleCurves)
export(tpp2dPlotQCpEC50)
export(tpp2dPlotQChist)
export(tpp2dRemoveZeroSias)
export(tpp2dSplineFitAndTest)
export(tpp2dTRReferenceObject) # define object
import(Biobase, except = combine) # conflict with gridExtra::combine
import(data.table, except = c(between, last, melt, first)) # conflict with dplyr and reshape2
import(dplyr, except = c(exprs)) # conflict with Biobase::exprs
import(ggplot2)
import(grid)
import(gridExtra, except = combine)
import(magrittr, except = extract)
import(openxlsx)
import(plyr, except = c(mutate, summarize, summarise, rename, arrange, id, desc, count, failwith)) # conflict with dplyr
import(splines)
import(tidyr)
import(VennDiagram)
import(VGAM, except = c(fill, AICc)) # conflict with tidyr's fill, and sme's AICc
importFrom(doParallel, registerDoParallel, stopImplicitCluster)
importFrom(foreach, '%dopar%', '%do%', foreach)
importFrom(futile.logger, flog.threshold, ERROR)
importFrom(knitr, kable)
importFrom(limma, squeezeVar)
importFrom(MASS, rlm)
importFrom(nls2, nls2)
importFrom(parallel, detectCores, stopCluster)
importFrom(reshape2, melt)
importFrom(rmarkdown, render)
importFrom(RColorBrewer, brewer.pal)
importFrom(RCurl, url.exists)
importFrom(purrr, map)
importFrom(stringr, str_to_title)
importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")  # The following lines are recommendations from R CMD check
importFrom("stats", "as.formula", "complete.cases", "contrasts", "df", "lm",
           "median", "na.exclude", "na.omit", "nls", "p.adjust", "pf",
           "qnorm", "quantile", "reshape", "runif", "sd", "setNames",
           "sigma", "uniroot")
importFrom("utils", "combn", "packageVersion", "read.delim",
           "read.table", "write.table")
importFrom("tibble", "as_tibble")
