CSsingle: A Unified Tool for Robust Decomposition of Bulk and Spatial Transcriptomic Data Across Diverse Single-Cell References.

ABSTRACT: We introduce CSsingle, a novel method that enhances the decomposition of bulk and spatial transcriptomic (ST) data by addressing key challenges in cellular heterogeneity. CSsingle applies cell size correction using ERCC spike-in controls, enabling it to account for variations in RNA content between cell types and achieve accurate bulk data deconvolution. In addition, it enables fine-scale analysis for ST data, advancing our understanding of tissue architecture and cellular interactions, particularly in complex microenvironments. We provide a unified tool for integrating bulk and ST with scRNA-seq data, advancing the study of complex biological systems and disease processes. The benchmark results demonstrate that CSsingle outperforms existing methods in accuracy and robustness. Validation u

SUBMITTER: Shen W 

PROVIDER: S-EPMC11030304 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature