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NAMESPACE
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117 lines (116 loc) · 3.21 KB
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# Generated by roxygen2: do not edit by hand
export(BanksyObject)
export(ClusterBanksy)
export(ComputeBanksy)
export(ConnectClusters)
export(NormalizeBanksy)
export(RunPCA)
export(RunUMAP)
export(ScaleBanksy)
export(SplitBanksy)
export(SubsetBanksy)
export(asBanksyObject)
export(getARI)
export(getBanksyMatrix)
export(plotARI)
export(plotAlluvia)
export(plotHeatmap)
export(plotReduction)
export(plotScree)
export(plotSpatial)
export(plotSpatialFeatures)
export(simulateDataset)
exportClasses(BanksyObject)
exportMethods("cell.locs<-")
exportMethods("custom.expr<-")
exportMethods("meta.data<-")
exportMethods("nbr.expr<-")
exportMethods("own.expr<-")
exportMethods("reduction<-")
exportMethods(cell.locs)
exportMethods(clust.names)
exportMethods(custom.expr)
exportMethods(head)
exportMethods(meta.data)
exportMethods(nbr.expr)
exportMethods(own.expr)
exportMethods(reduction)
exportMethods(show)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,`%v%`)
importFrom(ComplexHeatmap,anno_barplot)
importFrom(RcppHungarian,HungarianSolver)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(circlize,colorRamp2)
importFrom(data.table,`:=`)
importFrom(data.table,data.table)
importFrom(data.table,key)
importFrom(data.table,rbindlist)
importFrom(data.table,setDT)
importFrom(data.table,setkey)
importFrom(data.table,setnames)
importFrom(data.table,setorder)
importFrom(dbscan,kNN)
importFrom(dbscan,sNN)
importFrom(ggalluvial,StatStratum)
importFrom(ggalluvial,geom_flow)
importFrom(ggalluvial,geom_stratum)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,ensym)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_gradient2)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(grid,gpar)
importFrom(gridExtra,grid.arrange)
importFrom(igraph,as.undirected)
importFrom(igraph,cluster_louvain)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,membership)
importFrom(irlba,prcomp_irlba)
importFrom(leidenAlg,leiden.community)
importFrom(matrixStats,rowSds)
importFrom(matrixStats,rowVars)
importFrom(mclust,Mclust)
importFrom(mclust,adjustedRandIndex)
importFrom(mclust,mclustBIC)
importFrom(methods,new)
importFrom(methods,show)
importFrom(methods,validObject)
importFrom(pals,glasbey)
importFrom(pals,kelly)
importFrom(pals,polychrome)
importFrom(plyr,mapvalues)
importFrom(rlang,enquo)
importFrom(rlang,quo_get_expr)
importFrom(stats,aggregate)
importFrom(stats,dnorm)
importFrom(stats,kmeans)
importFrom(stats,median)
importFrom(stats,quantile)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(utils,combn)
importFrom(utils,head)
importFrom(utils,packageVersion)
importFrom(uwot,umap)