Heterogeneous pseudobulk simulation enables realistic benchmarking of cell-type deconvolution methods.

ABSTRACT:

Background

Computational cell type deconvolution enables the estimation of cell type abundance from bulk tissues and is important for understanding tissue microenviroment, especially in tumor tissues. With rapid development of deconvolution methods, many benchmarking studies have been published aiming for a comprehensive evaluation for these methods. Benchmarking studies rely on cell-type resolved single-cell RNA-seq data to create simulated pseudobulk datasets by adding individual cells-types in controlled proportions.

Results

In our work, we show that the standard application of this approach, which uses randomly selected single cells, regardless of the intrinsic difference between them, generates synthetic bulk expression values that lack appropriate biological variance.

SUBMITTER: Hu M 

PROVIDER: S-EPMC11218230 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature