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

In Methods in molecular biology (Clifton, N.J.)

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.

Steen Chloé B, Luca Bogdan A, Alizadeh Ash A, Gentles Andrew J, Newman Aaron M

2023

Cell states, Ecosystems, Ecotypes, Single-cell RNA sequencing, Spatial transcriptomics, Tissue heterogeneity, Transcriptomics, Tumor microenvironment