# Generated by roxygen2: do not edit by hand

S3method(MSstatsContrastMatrix,character)
S3method(MSstatsContrastMatrix,data.frame)
S3method(MSstatsContrastMatrix,list)
S3method(MSstatsContrastMatrix,matrix)
export(DIANNtoMSstatsFormat)
export(DIAUmpiretoMSstatsFormat)
export(FragPipetoMSstatsFormat)
export(MSstatsContrastMatrix)
export(MSstatsGroupComparison)
export(MSstatsGroupComparisonOutput)
export(MSstatsGroupComparisonSingleProtein)
export(MSstatsHandleMissing)
export(MSstatsMergeFractions)
export(MSstatsNormalize)
export(MSstatsPrepareForDataProcess)
export(MSstatsPrepareForGroupComparison)
export(MSstatsPrepareForSummarization)
export(MSstatsQualityMetricsPlot)
export(MSstatsSelectFeatures)
export(MSstatsSummarizationOutput)
export(MSstatsSummarizeSingleLinear)
export(MSstatsSummarizeSingleTMP)
export(MSstatsSummarizeWithMultipleCores)
export(MSstatsSummarizeWithSingleCore)
export(MZMinetoMSstatsFormat)
export(MaxQtoMSstatsFormat)
export(OpenMStoMSstatsFormat)
export(OpenSWATHtoMSstatsFormat)
export(PDtoMSstatsFormat)
export(ProgenesistoMSstatsFormat)
export(SDRFtoAnnotation)
export(SkylinetoMSstatsFormat)
export(SpectronauttoMSstatsFormat)
export(checkRepeatedDesign)
export(dataProcess)
export(dataProcessPlots)
export(designSampleSize)
export(designSampleSizePlots)
export(extractSDRF)
export(getProcessed)
export(getSamplesInfo)
export(getSelectedProteins)
export(groupComparison)
export(groupComparisonPlots)
export(groupComparisonQCPlots)
export(makePeptidesDictionary)
export(modelBasedQCPlots)
export(quantification)
export(savePlot)
export(theme_msstats)
export(validateAnnotation)
import(data.table)
import(ggplot2)
import(limma)
import(lme4)
importFrom(BiocParallel,
  bpisup,
  bplapply,
  bpnworkers,
  bpprogressbar,
  bpstart,
  bpstop
)
importFrom(MASS,rlm)
importFrom(MSstatsConvert,
  DIANNtoMSstatsFormat,
  DIAUmpiretoMSstatsFormat,
  FragPipetoMSstatsFormat,
  MSstatsBalancedDesign,
  MSstatsClean,
  MSstatsImport,
  MSstatsLogsSettings,
  MSstatsMakeAnnotation,
  MSstatsPreprocess,
  MZMinetoMSstatsFormat,
  MaxQtoMSstatsFormat,
  OpenMStoMSstatsFormat,
  OpenSWATHtoMSstatsFormat,
  PDtoMSstatsFormat,
  ProgenesistoMSstatsFormat,
  SkylinetoMSstatsFormat,
  SpectronauttoMSstatsFormat
)
importFrom(Rcpp,sourceCpp)
importFrom(RhpcBLASctl,blas_set_num_threads)
importFrom(data.table,
  as.data.table,
  data.table,
  fifelse,
  melt,
  rbindlist,
  setDT,
  setDTthreads,
  uniqueN
)
importFrom(ggrepel,geom_text_repel)
importFrom(gplots,heatmap.2)
importFrom(grDevices,
  dev.off,
  hcl,
  pdf
)
importFrom(graphics,
  axis,
  image,
  legend,
  mtext,
  par,
  plot,
  plot.new,
  title
)
importFrom(htmltools,
  div,
  save_html,
  tagList
)
importFrom(limma,squeezeVar)
importFrom(lme4,lmer)
importFrom(marray,maPalette)
importFrom(matter,SnowfastParam)
importFrom(methods,is)
importFrom(parallel,
  clusterExport,
  makeCluster,
  parLapply,
  stopCluster
)
importFrom(plotly,
  add_trace,
  ggplotly,
  layout,
  plot_ly,
  style,
  subplot
)
importFrom(preprocessCore,normalize.quantiles)
importFrom(rlang,.data)
importFrom(stats,
  dist,
  dnorm,
  fitted,
  formula,
  hclust,
  lm,
  lm.fit,
  loess,
  median,
  model.frame,
  model.matrix,
  model.response,
  na.omit,
  p.adjust,
  pnorm,
  predict,
  qbinom,
  qnorm,
  qt,
  quantile,
  resid,
  residuals,
  sd,
  vcov,
  xtabs
)
importFrom(survival,
  Surv,
  survreg
)
importFrom(utils,
  combn,
  sessionInfo,
  setTxtProgressBar,
  txtProgressBar
)
useDynLib(MSstats, .registration=TRUE)
