scp/NAMESPACE at master · UCLouvain-CBIO/scp · GitHub

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# Generated by roxygen2: do not edit by hand

export("scpModelFilterThreshold<-")
export(addReducedDims)
export(computeSCR)
export(cumulativeSensitivityCurve)
export(divideByReference)
export(jaccardIndex)
export(medianCVperCell)
export(normalizeSCP)
export(pep2qvalue)
export(predictSensitivity)
export(readSCP)
export(readSCPfromDIANN)
export(readSingleCellExperiment)
export(reportMissingValues)
export(scpAnnotateResults)
export(scpComponentAggregate)
export(scpComponentAnalysis)
export(scpComponentBiplot)
export(scpComponentPlot)
export(scpDifferentialAggregate)
export(scpDifferentialAnalysis)
export(scpKeepEffect)
export(scpModelComponentMethods)
export(scpModelEffects)
export(scpModelFilterNPRatio)
export(scpModelFilterPlot)
export(scpModelFilterThreshold)
export(scpModelFormula)
export(scpModelInput)
export(scpModelNames)
export(scpModelResiduals)
export(scpModelWorkflow)
export(scpRemoveBatchEffect)
export(scpVarianceAggregate)
export(scpVarianceAnalysis)
export(scpVariancePlot)
export(scpVolcanoPlot)
exportClasses(ScpModel)
exportClasses(ScpModelFit)
import(QFeatures)
import(RColorBrewer)
import(SingleCellExperiment)
import(SummarizedExperiment)
import(ggplot2)
importFrom(IHW,
  adj_pvalues,
  ihw
)
importFrom(MsCoreUtils,normalize_matrix)
importFrom(MultiAssayExperiment,
  "experiments<-",
  ExperimentList
)
importFrom(QFeatures,
  aggregateFeatures,
  readSummarizedExperiment,
  reduceDataFrame
)
importFrom(S4Vectors,
  "metadata<-",
  DataFrame,
  List,
  endoapply,
  metadata
)
importFrom(SingleCellExperiment,"reducedDims<-")
importFrom(SummarizedExperiment,
  "assays<-",
  assay,
  assayNames,
  assays,
  colData,
  rowData
)
importFrom(ggrepel,
  geom_label_repel,
  geom_text_repel
)
importFrom(matrixStats,colMedians)
importFrom(metapod,combineGroupedPValues)
importFrom(methods,
  as,
  new
)
importFrom(nipals,nipals)
importFrom(stats,
  as.formula,
  median,
  model.matrix,
  nls,
  p.adjust,
  predict,
  pt,
  reformulate,
  sd,
  terms,
  var
)
importFrom(utils,
  setTxtProgressBar,
  txtProgressBar
)