- Matthew N Bernstein: Morgridge Institute for Research, Madison, WI 53715, USA.
- Colin N Dewey: Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, WI 53792, USA.
Cell type annotation is important in the analysis of single-cell RNA-seq data. CellO is a machine-learning-based tool for annotating cells using the Cell Ontology, a rich hierarchy of known cell types. We provide a protocol for using the CellO Python package to annotate human cells. We demonstrate how to use CellO in conjunction with Scanpy, a Python library for performing single-cell analysis, annotate a lung tissue data set, interpret its hierarchically structured cell type annotations, and create publication-ready figures. For complete details on the use and execution of this protocol, please refer to Bernstein et al. (2021).