{"SingleCellExperiment":"input@assays$data$logcounts","URD":"input@logupx.data","FunctionalSingleCellExperiment":"input@ExperimentList$rnaseq@assays$data$logcounts","Seurat":"input@assays$RNA@data","CellDataSet":"do.call(function(x) {row.names(x) <- input@featureData@data$gene_short_name; return(x)}, list(input@assayData$exprs))","H5File":"{mat <- input[[\"layers/norm_data\"]][,];\ncolnames(mat) <- input[[\"row_attrs/gene_names\"]][];\nrownames(mat) <- input[[\"col_attrs/cell_names\"]][];\nmat <- t(mat);\nreturn(mat)}","_row":"expr"}
{"SingleCellExperiment":"as.data.frame(input@colData)","URD":"input@meta","FunctionalSingleCellExperiment":"input@ExperimentList$rnaseq@colData","Seurat":"input@meta.data","CellDataSet":"as.data.frame(input@phenoData@data)","H5File":"{l <- input$ls(recursive=TRUE);\ns <- l[,1][stringr::str_detect(l[,1], \"col_attrs/\")];\ns2 <- sapply(s, FUN=function(x) {input[[x]][]});\ncolnames(s2) <- stringr::str_remove(colnames(s2),\"col_attrs/\");\nmeta <- tibble::column_to_rownames(as.data.frame(s2), \"cell_names\");\nreturn(meta)}","_row":"meta"}
{"SingleCellExperiment":"NULL","URD":"input@var.genes","FunctionalSingleCellExperiment":"NULL","Seurat":"input@assays$RNA@var.features","CellDataSet":"as.character(input@featureData@data$gene_short_name[input@featureData@data$use_for_ordering == T])","H5File":"NULL","_row":"var"}
{"SingleCellExperiment":"cell_type1","URD":"cluster","FunctionalSingleCellExperiment":"leiden_cluster","Seurat":"RNA_snn_res.1","CellDataSet":"Main_Cluster","H5File":"orig.ident","_row":"col"}