# Generated by roxygen2: do not edit by hand

export(PipelineDefinition)
export(addPipelineStep)
export(aggregatePipelineResults)
export(buildCombMatrix)
export(checkPipelinePackages)
export(colCenterScale)
export(dea_evalPlot_curve)
export(dea_pipeline)
export(defaultStepAggregation)
export(evalHeatmap)
export(evaluateClustering)
export(evaluateDEA)
export(evaluateDimRed)
export(evaluateNorm)
export(farthestPoint)
export(getQualitativePalette)
export(match_evaluate_multiple)
export(mergePipelineResults)
export(mockPipeline)
export(parsePipNames)
export(plotElapsed)
export(readPipelineResults)
export(runPipeline)
export(scrna_describeDatasets)
export(scrna_evalPlot_filtering)
export(scrna_evalPlot_overall)
export(scrna_evalPlot_silh)
export(scrna_pipeline)
exportClasses(PipelineDefinition)
exportMethods("defaultArguments<-")
exportMethods("stepFn<-")
exportMethods(arguments)
exportMethods(defaultArguments)
exportMethods(stepFn)
import(BiocParallel)
import(ComplexHeatmap)
import(S4Vectors)
import(Seurat)
import(SingleCellExperiment)
import(ggplot2)
import(intrinsicDimension)
import(methods)
import(scales)
import(scater)
import(scran)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(Matrix,rowMeans)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rtsne,Rtsne)
importFrom(S4Vectors,DataFrame)
importFrom(Seurat,GetAssayData)
importFrom(Seurat,Stdev)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(aricode,clustComp)
importFrom(circlize,colorRamp2)
importFrom(clue,solve_LSAP)
importFrom(cluster,silhouette)
importFrom(cowplot,plot_grid)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(grid,gpar)
importFrom(grid,grid.text)
importFrom(knitr,opts_current)
importFrom(matrixStats,rowMedians)
importFrom(matrixStats,rowMins)
importFrom(methods,is)
importFrom(methods,slot)
importFrom(randomcoloR,distinctColorPalette)
importFrom(reshape2,melt)
importFrom(stats,as.formula)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(utils,installed.packages)
importFrom(utils,sessionInfo)
importFrom(utils,type.convert)
importFrom(uwot,umap)
importFrom(viridisLite,inferno)
importMethodsFrom(methods,show)