Benchmarking second-generation methods for cell-type deconvolution of transcriptomic data

Abstract

In silico cell-type deconvolution from bulk transcriptomics data is a powerful technique to gain insights into the cellular composition of complex tissues. While first-generation methods used precomputed expression signatures covering limited cell types and tissues, second-generation tools use single-cell RNA sequencing data to build custom signatures for deconvoluting arbitrary cell types, tissues, and organisms. This flexibility poses significant challenges in assessing their deconvolution performance. Here, we comprehensively benchmark second-generation tools, disentangling different sources of variation and bias using a diverse panel of real and simulated data. Our study highlights the strengths, limitations, and complementarity of state-of-the-art tools shedding light on how different data characteristics and confounders impact deconvolution performance. We provide the scientific community with an ecosystem of tools and resources,omnideconv, simplifying the application, benchmarking, and optimization of deconvolution methods.