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Updated: Jan 9, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
Published on: January 10, 2019
Protocol for inferring cell type relationships and linking genomic annotations to cell type hierarchies using
Zhirui Hu1, Pawel F Przytycki2, Katherine S Pollard3
1Gladstone Institute of Data Science & Biotechnology, 1650 Owens Street, San Francisco, CA 94158, USA.
Abstract:
Single-cell multiomic data reveal cell type-specific regulatory mechanisms, but comparing hierarchies and regulatory programs across related cell types is challenging. Here, we present a protocol for integrating single-cell data to infer cell type relationships and label genomic annotations within cell type hierarchies using CellWalker2, a graph diffusion-based framework. We describe steps for cell labeling; comparing cell type hierarchies; mapping regulatory elements or transcription factors onto cell type hierarchies; and assessing statistical significance, using human blood and brain datasets. For complete details on the use and execution of this protocol, please refer to Hu et al.1.
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