Putative cell type discovery from single-cell gene expression data.

We present the Single-Cell Clustering Assessment Framework, a method for the automated identification of putative cell types from single-cell RNA sequencing (scRNA-seq) data. By iteratively applying a machine learning approach to a given set of cells, we simultaneously identify distinct cell groups and a weighted list of feature genes for each group. The differentially expressed feature genes discriminate the given cell group from other cells. Each such group of cells corresponds to a putative cell type or state, characterized by the feature genes as markers. Benchmarking using expert-annotated scRNA-seq datasets shows that our method automatically identifies the ‘ground truth’ cell assignments with high accuracy. SCCAF automates the discovery of putative cell types and their feature genes using scRNA-seq data.