EcoTyper
method
transcriptomics
Definition
EcoTyper is a computational framework for identifying cell states and multicellular ecotypes from single-cell and bulk transcriptomic data.
What It Gives
- Cell states within major cell types
- Co-occurring cell-state communities
- Tumour or carcinoma ecotypes
- Links between ecotypes and clinical outcomes
Main Strength
EcoTyper connects single-cell-defined cell states to large bulk RNA-seq cohorts, making clinical association analysis more scalable.
Main Limitation
The original EcoTyper framework does not directly use tissue spatial coordinates. It can infer co-occurring cell states, but not whether those states are spatially colocalized in tumour core, tumour margin, or stroma.
In Papers
- Luca et al. 2021 Cell is the key source for tumour ecotypes.
- Zhang et al. 2026 extends the ecotype idea into spatial ecotypes.