Slots: raw.data The raw project data data The normalized expression matrix (log-scale) scale.data scaled (default is z-scoring each gene) expression matrix; used for dimmensional reduction and heatmap visualization var.genes Vector of genes exhibiting high variance across single cells is.expr Expression threshold to determine if a gene is expressed (0 by default) ident THe 'identity class' for each cell meta.data Contains meta-information about each cell, starting with number of genes detected (nGene) and the original identity class (orig.ident); more information is added using AddMetaData project.name Name of the project (for record keeping) dr List of stored dimmensional reductions; named by technique assay List of additional assays for multimodal analysis; named by technique hvg.info The output of the mean/variability analysis for all genes imputed Matrix of imputed gene scores cell.names Names of all single cells (column names of the expression matrix) cluster.tree List where the first element is a phylo object containing the phylogenetic tree relating different identity classes snn Spare matrix object representation of the SNN graph calc.params Named list to store all calculation-related parameter choices kmeans Stores output of gene-based clustering from DoKMeans spatial Stores internal data and calculations for spatial mapping of single cells misc Miscellaneous spot to store any data alongisde the object (for example, gene lists) version Version of package used in object creation