# Generated by roxygen2: do not edit by hand

export(.pp_organize_effects)
export(filter_se_missing)
export(impute_se)
export(plot_deregulogram)
export(plot_volcano_customized)
export(run_proteomics_pipeline)
export(test_limma_customized)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,
  SummarizedExperiment,
  assay,
  colData,
  rowData
)
importFrom(data.table,
  dcast.data.table,
  melt.data.table,
  setDT
)
importFrom(ggplot2,
  aes,
  element_blank,
  element_line,
  geom_hline,
  geom_point,
  geom_text,
  geom_vline,
  ggplot,
  labs,
  scale_color_manual,
  theme,
  theme_bw,
  theme_minimal
)
importFrom(ggrepel,
  geom_label_repel,
  geom_text_repel
)
importFrom(grDevices,
  dev.off,
  pdf
)
importFrom(grid,unit)
importFrom(limma,
  contrasts.fit,
  duplicateCorrelation,
  eBayes,
  lmFit,
  makeContrasts,
  topTable
)
importFrom(methods,is)
importFrom(stats,
  as.formula,
  complete.cases,
  formula,
  median,
  model.matrix,
  p.adjust,
  relevel,
  rnorm,
  sd,
  setNames,
  update
)
importFrom(utils,
  globalVariables,
  read.csv,
  read.delim,
  read.table,
  write.csv
)
