* sc_QC (filter cells, scale and remove variation associated to: UMI; % mitochondrial genes; S; G2M phase score, identify most variable genes and run PCA on them
* sc_Cluster (perform tSNE and cluster using graph*based approach)
* sc_PC.Score.Stress (PCA analysis of stress gene signature, projecction to PC1 used as "Stress Score", stressed cells and clusters removed cells re*clustered)
* sc_QuSAGE.Lineage (clusters correlated to prostate population RNA-Seq DEGs of Epithelia and Fibromuscular Stroma to assign those identities to those clusters)
* sc_QuSAGE.Epi (Epithelial clusters correlated to prostate population RNA-Seq DEGs of Basal, Luminal, and "Other" Epithelia to assign those identities to those clusters)
* sc_QuSAGE.St (Stromal clusters correlated to external DEGs of Endothelial Cells, Smooth Muscle Cells, and Fibroblasts to assign those identities to those clusters)
* sc_LineageSubClust (separate identified Epithelia, and Stroma + Lineage Unknown cells, and recluster them independently)
* sc_QuSAGE.EpiSubClust (Epithelial clusters correlated to DWS generated prostate population RNA-Seq DEGs of Basal, Luminal, and "Other" Epithelia, Lung Map generated Epithelial, C2 KEGG, and C5 GO BP genesets, to assign those identities to those clusters)
* sc_QuSAGE.StSubClust (Stromal and Lineage Unknown clusters correlated to external DEGs of Endothelial Cells, Smooth Muscle Cells, and Fibroblasts, Lung Map generated Epithelial, C2 KEGG, and C5 GO BP genesets, to assign those identities to those clusters)
* sc_MergeSubClust (merge identities of Eithelial and non-Epithelial clusters from QuSAGE)
* sc_PC.Score.NE (PCA analysis of Neurocrine Epithelia protein marker signature, projecction to PC1 used as "NE Score", highest scoring cells identified as Neuroendocrine Cells)
* sc_QuSAGE.LGEA.Epi (Epithelial clusters correlated to top 20 DEGs from scRNA-seq of human lung Basal Cells, Alveolar Type 2 Cells, Club/Goblet Cells to determine similarity to lung epithelial cell types)
* sc_QuSAGE.LGEA.St (Stromal clusters correlated to human orthologs of mouse lung stromal DEGs from scRNA*seq to determine similarity to:)
* Proliferative Fibrobblasts
* Myofibroblast/Smooth Muscle-Like Cells
* Matrix Fibroblasts
* Endothelial Cells
* Myeloid/Immune Cells
* sc_DEG (generate DEG lists between important cell types and predict surface and nuclear markers from them)
* sc_Table (produce tables of population differences between samples)
