Galaxy single-cell & spatial omics community update: Navigating new frontiers in 2025

Abstract

Single-cell omics, named Method of the Year three times, have revolutionized biological research by enabling the high-resolution exploration of cellular heterogeneity and molecular processes. Initially centered on transcriptomics, this rapidly evolving field now ranges from multiomics to spatial analysis, with expanding customization options. The ubiquity of such analyses and the lack of a unified pipeline necessitate the development of scalable, flexible, and integrated tools and workflows. The Galaxy platform has responded to these technological advancements, extending its repertoire of freely accessible tools and workflows, backed by expert-reviewed and user-informed training resources to empower researchers to perform and interpret their own analyses. With more than 175 tools, 120 training resources, and 300,000 jobs running at the time of writing, this process has culminated in the development of Galaxy single-cell and spatial omics community (SPOC), designed to promote global collaboration in advancing usable, reproducible, accessible, and sustainable single-cell and spatial omics research.