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Profiling Cellular Ecosystems at Single-Cell Resolution and at Scale with EcoTyper.

Profiling Cellular Ecosystems at Single-Cell Resolution and at Scale with EcoTyper. Methods in molecular biology (Clifton, N.J.) Steen, C. B., Luca, B. A., Alizadeh, A. A., Gentles, A. J., Newman, A. M. 2023; 2629: 43-71

Abstract

Tissues are composed of diverse cell types and cellular states that organize into distinct ecosystems with specialized functions. EcoTyper is a collection of machine learning tools for the large-scale delineation of cellular ecosystems and their constituent cell states from bulk, single-cell, and spatially resolved gene expression data. In this chapter, we provide a primer on EcoTyper and demonstrate its use for the discovery and recovery of cell states and ecosystems from healthy and diseased tissue specimens.

View details for DOI 10.1007/978-1-0716-2986-4_4

View details for PubMedID 36929073

View details for PubMedCentralID 9067608