scCompass: An Integrated Multi-Species scRNA-seq Database for AI-Ready

Adv Sci (Weinh). 2025 May 2:e2500870. doi: 10.1002/advs.202500870. Online ahead of print.

ABSTRACT

Emerging single-cell sequencing technology has generated large amounts of data, allowing analysis of cellular dynamics and gene regulation at the single-cell resolution. Advances in artificial intelligence enhance life sciences research by delivering critical insights and optimizing data analysis processes. However, inconsistent data processing quality and standards remain to be a major challenge. Here scCompass is proposed, which provides a comprehensive resource designed to build large-scale, multi-species, and model-friendly single-cell data collection. By applying standardized data pre-processing, scCompass integrates and curates transcriptomic data from nearly 105 million single cells across 13 species. Using this extensive dataset, it is able to identify stable expression genes (SEGs) and organ-specific expression genes (OSGs) in humans and mice. Different scalable datasets are provided that can be easily adapted for AI model training and the pretrained checkpoints with state-of-the-art single-cell foundation models. In summary, scCompass is highly efficient and scalable database for AI-ready, which combined with user-friendly data sharing, visualization, and online analysis, greatly simplifies data access and exploitation for researchers in single-cell biology (http://www.bdbe.cn/kun).

PMID:40317650 | DOI:10.1002/advs.202500870