FastCCC: a permutation-free framework for scalable, robust, and reference-based cell-cell communication analysis in single cell transcriptomics studies.

ABSTRACT: Detecting cell-cell communications (CCCs) in single-cell transcriptomics studies is fundamental for understanding the function of multicellular organisms. Here, we introduce FastCCC, a permutation-free framework that enables scalable, robust, and reference-based analysis for identifying critical CCCs and uncovering biological insights. FastCCC relies on fast Fourier transformation-based convolution to compute p-values analytically without permutations, introduces a modular algebraic operation framework to capture a broad spectrum of CCC patterns, and can leverage atlas-scale single cell references to enhance CCC analysis on user-collected datasets. To support routine reference-based CCC analysis, we constructed the first human CCC reference panel, encompassing 19 distinct tissue types, ove

SUBMITTER: Hou S 

PROVIDER: S-EPMC12749929 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature