# Generated by roxygen2: do not edit by hand

export("%>%")
export("assayCollapsed<-")
export("colDataCollapsed<-")
export("groups<-")
export("replicates<-")
export("timeSeries<-")
export("timepoints<-")
export()
export(TimeSeriesExperiment)
export(addLags)
export(assayCollapsed)
export(assignClusterStatic)
export(clusterAssignment)
export(clusterData)
export(clusterMap)
export(clusterTimeSeries)
export(colDataCollapsed)
export(collapseReplicates)
export(dataToTimeSeries)
export(differentialExpression)
export(dimensionReduction)
export(filterFeatures)
export(groups)
export(makeTimeSeries)
export(makeTimeSeriesExperimentFromExpressionSet)
export(makeTimeSeriesExperimentFromSummarizedExperiment)
export(meltMatrix)
export(normalizeData)
export(pathwayEnrichment)
export(plotEnrichment)
export(plotHeatmap)
export(plotSamplePCA)
export(plotTimeSeries)
export(plotTimeSeriesClusters)
export(plotTimeSeriesPCA)
export(replicates)
export(runPCA)
export(timeSeries)
export(timepointDE)
export(timepoints)
export(trajectoryDE)
export(varianceStabilization)
exportClasses(TimeSeriesExperiment)
exportMethods("assayCollapsed<-")
exportMethods("colData<-")
exportMethods("colDataCollapsed<-")
exportMethods("colnames<-")
exportMethods("groups<-")
exportMethods("replicates<-")
exportMethods("rowData<-")
exportMethods("rownames<-")
exportMethods("timeSeries<-")
exportMethods("timepoints<-")
exportMethods(assayCollapsed)
exportMethods(clusterAssignment)
exportMethods(clusterMap)
exportMethods(colDataCollapsed)
exportMethods(differentialExpression)
exportMethods(dimensionReduction)
exportMethods(groups)
exportMethods(replicates)
exportMethods(show)
exportMethods(timeSeries)
exportMethods(timepoints)
import(methods)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(DESeq2,varianceStabilizingTransformation)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,setValidity2)
importFrom(SummarizedExperiment,Assays)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,makeSummarizedExperimentFromExpressionSet)
importFrom(SummarizedExperiment,rowData)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,contains)
importFrom(dplyr,data_frame)
importFrom(dplyr,desc)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,starts_with)
importFrom(dplyr,summarise)
importFrom(dplyr,summarise_all)
importFrom(dplyr,summarize_all)
importFrom(dplyr,top_n)
importFrom(dynamicTreeCut,cutreeDynamicTree)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(graphics,legend)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(limma,eBayes)
importFrom(limma,goana)
importFrom(limma,kegga)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(magrittr,"%>%")
importFrom(methods,"slot<-")
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(methods,validObject)
importFrom(proxy,dist)
importFrom(stats,aggregate)
importFrom(stats,cutree)
importFrom(stats,hclust)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,prcomp)
importFrom(stats,sd)
importFrom(tibble,add_row)
importFrom(tibble,as_data_frame)
importFrom(tibble,column_to_rownames)
importFrom(tibble,remove_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,gather)
importFrom(tidyr,spread)
importFrom(utils,installed.packages)
importFrom(vegan,adonis)
importFrom(viridis,scale_color_viridis)
importFrom(viridis,scale_fill_viridis)
importFrom(viridis,viridis)
importMethodsFrom(S4Vectors,"mcols<-")
importMethodsFrom(SummarizedExperiment,"assays<-")
importMethodsFrom(SummarizedExperiment,"colData<-")
importMethodsFrom(SummarizedExperiment,"rowData<-")
importMethodsFrom(SummarizedExperiment,assays)
importMethodsFrom(SummarizedExperiment,colData)
importMethodsFrom(SummarizedExperiment,rowData)
importMethodsFrom(SummarizedExperiment,show)
