Supervised classification enables rapid annotation of cell atlases

Single cell technologies for profiling tissues or even entire organisms are rapidly being adopted. However, the manual process by which cell types are typically annotated in the resulting data is labor-intensive and increasingly rate-limiting for the field. Here we describe Garnett, an algorithm and accompanying software for rapidly annotating cell types in scRNA-seq and scATAC-seq datasets, based on an interpretable, hierarchical markup language of cell type-specific genes. Garnett successfully classifies cell types in tissue and whole organism datasets, as well as across species.