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NAMESPACE
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231 lines (230 loc) · 7.08 KB
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# Generated by roxygen2: do not edit by hand
S3method(GetTDR,Seurat)
S3method(GetTDR,SingleCellExperiment)
S3method(GetTDR,SummarizedExperiment)
S3method(GetTDR,default)
S3method(RunTDR,DelayedMatrix)
S3method(RunTDR,HDF5AnnData)
S3method(RunTDR,IterableMatrix)
S3method(RunTDR,Seurat)
S3method(RunTDR,SingleCellExperiment)
S3method(RunTDR,character)
S3method(RunTDR,cytoset)
S3method(RunTDR,default)
S3method(RunTDR,dgCMatrix)
S3method(RunTDR,flowSet)
S3method(SetTDR,Seurat)
S3method(SetTDR,SingleCellExperiment)
S3method(SetTDR,SummarizedExperiment)
S3method(SetTDR,default)
S3method(as.SummarizedExperiment,TDRObj)
S3method(celltyping,Seurat)
S3method(celltyping,SingleCellExperiment)
S3method(celltyping,SummarizedExperiment)
S3method(celltyping,TDRObj)
S3method(get.density,TDRObj)
S3method(get.embedding,Seurat)
S3method(get.embedding,SingleCellExperiment)
S3method(get.embedding,SummarizedExperiment)
S3method(get.embedding,TDRObj)
S3method(get.features,Seurat)
S3method(get.features,SingleCellExperiment)
S3method(get.features,SummarizedExperiment)
S3method(get.features,TDRObj)
S3method(get.graph,Seurat)
S3method(get.graph,SingleCellExperiment)
S3method(get.graph,SummarizedExperiment)
S3method(get.graph,TDRObj)
S3method(get.landmarks,Seurat)
S3method(get.landmarks,SingleCellExperiment)
S3method(get.landmarks,SummarizedExperiment)
S3method(get.landmarks,TDRObj)
S3method(get.lm,Seurat)
S3method(get.lm,SingleCellExperiment)
S3method(get.lm,SummarizedExperiment)
S3method(get.lm,TDRObj)
S3method(get.map,Seurat)
S3method(get.map,SingleCellExperiment)
S3method(get.map,SummarizedExperiment)
S3method(get.map,TDRObj)
S3method(get.markerDE,Seurat)
S3method(get.markerDE,SingleCellExperiment)
S3method(get.markerDE,SummarizedExperiment)
S3method(get.markerDE,TDRObj)
S3method(get.pbDE,Seurat)
S3method(get.pbDE,SingleCellExperiment)
S3method(get.pbDE,SummarizedExperiment)
S3method(get.pbDE,TDRObj)
S3method(get.plsD,Seurat)
S3method(get.plsD,SingleCellExperiment)
S3method(get.plsD,SummarizedExperiment)
S3method(get.plsD,TDRObj)
S3method(get.subset,Seurat)
S3method(get.subset,SingleCellExperiment)
S3method(get.subset,SummarizedExperiment)
S3method(get.subset,TDRObj)
S3method(goi.summary,Seurat)
S3method(goi.summary,SingleCellExperiment)
S3method(goi.summary,SummarizedExperiment)
S3method(goi.summary,TDRObj)
S3method(import_cell_annotations,Seurat)
S3method(import_cell_annotations,SingleCellExperiment)
S3method(import_cell_annotations,SummarizedExperiment)
S3method(import_cell_annotations,TDRObj)
S3method(list_celltyping_solutions,Seurat)
S3method(list_celltyping_solutions,SingleCellExperiment)
S3method(list_celltyping_solutions,SummarizedExperiment)
S3method(list_celltyping_solutions,TDRObj)
S3method(lm.cluster,Seurat)
S3method(lm.cluster,SingleCellExperiment)
S3method(lm.cluster,SummarizedExperiment)
S3method(lm.cluster,TDRObj)
S3method(plot2Markers,Seurat)
S3method(plot2Markers,SingleCellExperiment)
S3method(plot2Markers,SummarizedExperiment)
S3method(plot2Markers,TDRObj)
S3method(plotBeeswarm,Seurat)
S3method(plotBeeswarm,SingleCellExperiment)
S3method(plotBeeswarm,SummarizedExperiment)
S3method(plotBeeswarm,TDRObj)
S3method(plotDEA,Seurat)
S3method(plotDEA,SingleCellExperiment)
S3method(plotDEA,SummarizedExperiment)
S3method(plotDEA,TDRObj)
S3method(plotDensity,Seurat)
S3method(plotDensity,SingleCellExperiment)
S3method(plotDensity,SummarizedExperiment)
S3method(plotDensity,TDRObj)
S3method(plotHeatmap,Seurat)
S3method(plotHeatmap,SingleCellExperiment)
S3method(plotHeatmap,SummarizedExperiment)
S3method(plotHeatmap,TDRObj)
S3method(plotMarkerDE,Seurat)
S3method(plotMarkerDE,SingleCellExperiment)
S3method(plotMarkerDE,SummarizedExperiment)
S3method(plotMarkerDE,TDRObj)
S3method(plotPCA,Seurat)
S3method(plotPCA,SingleCellExperiment)
S3method(plotPCA,SummarizedExperiment)
S3method(plotPCA,TDRObj)
S3method(plotPbDE,Seurat)
S3method(plotPbDE,SingleCellExperiment)
S3method(plotPbDE,SummarizedExperiment)
S3method(plotPbDE,TDRObj)
S3method(plotPlsD,Seurat)
S3method(plotPlsD,SingleCellExperiment)
S3method(plotPlsD,SummarizedExperiment)
S3method(plotPlsD,TDRObj)
S3method(plotPlsDHeatmap,Seurat)
S3method(plotPlsDHeatmap,SingleCellExperiment)
S3method(plotPlsDHeatmap,SummarizedExperiment)
S3method(plotPlsDHeatmap,TDRObj)
S3method(plotSampleEmbedding,Seurat)
S3method(plotSampleEmbedding,SingleCellExperiment)
S3method(plotSampleEmbedding,SummarizedExperiment)
S3method(plotSampleEmbedding,TDRObj)
S3method(plotSamplePCA,Seurat)
S3method(plotSamplePCA,SingleCellExperiment)
S3method(plotSamplePCA,SummarizedExperiment)
S3method(plotSamplePCA,TDRObj)
S3method(plotTradPerc,Seurat)
S3method(plotTradPerc,SingleCellExperiment)
S3method(plotTradPerc,SummarizedExperiment)
S3method(plotTradPerc,TDRObj)
S3method(plotTradStats,Seurat)
S3method(plotTradStats,SingleCellExperiment)
S3method(plotTradStats,SummarizedExperiment)
S3method(plotTradStats,TDRObj)
S3method(plotUMAP,Seurat)
S3method(plotUMAP,SingleCellExperiment)
S3method(plotUMAP,SummarizedExperiment)
S3method(plotUMAP,TDRObj)
S3method(recluster,Seurat)
S3method(recluster,SingleCellExperiment)
S3method(recluster,SummarizedExperiment)
S3method(recluster,TDRObj)
S3method(set_active_celltyping,Seurat)
S3method(set_active_celltyping,SingleCellExperiment)
S3method(set_active_celltyping,SummarizedExperiment)
S3method(set_active_celltyping,TDRObj)
S3method(set_active_clustering,Seurat)
S3method(set_active_clustering,SingleCellExperiment)
S3method(set_active_clustering,SummarizedExperiment)
S3method(set_active_clustering,TDRObj)
export(GetTDR)
export(RunTDR)
export(SetTDR)
export(TDRObj)
export(as.SummarizedExperiment)
export(celltyping)
export(fetch_trajectory_data)
export(get.cellmap)
export(get.cells)
export(get.cells.SCE)
export(get.cells.Seurat)
export(get.cells.Seurat5)
export(get.cells.list.mat)
export(get.dea)
export(get.density)
export(get.embedding)
export(get.features)
export(get.graph)
export(get.landmarks)
export(get.lm)
export(get.map)
export(get.marker)
export(get.markerDE)
export(get.meta)
export(get.meta.HDF5AnnData)
export(get.meta.SCE)
export(get.meta.Seurat)
export(get.meta.Seurat5)
export(get.pbDE)
export(get.plsD)
export(get.subset)
export(goi.summary)
export(import_cell_annotations)
export(is.TDRObj)
export(list_celltyping_solutions)
export(lm.cluster)
export(plot2Markers)
export(plotBeeswarm)
export(plotDEA)
export(plotDensity)
export(plotHeatmap)
export(plotMarkerDE)
export(plotPCA)
export(plotPbDE)
export(plotPlsD)
export(plotPlsDHeatmap)
export(plotSampleEmbedding)
export(plotSamplePCA)
export(plotTradPerc)
export(plotTradStats)
export(plotUMAP)
export(recluster)
export(scatterPlot)
export(set_active_celltyping)
export(set_active_clustering)
export(setup.lm.obj)
export(setup.tdr.obj)
export(simulate_DA_data)
export(simulate_DE_data)
export(tdr_cache_cleanup)
export(tdr_cache_info)
export(tdr_cache_validate)
exportClasses(TDRObj)
import(Matrix)
import(patchwork)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setAs)
importFrom(methods,setClass)
importFrom(methods,setMethod)
importFrom(methods,setReplaceMethod)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(methods,validObject)