ATLAS: a scverse-compatible package for multi-omic single-cell trajectory inference integration

Single-cell trajectory inference is widely used to study cellular differentiation and fate decisions, yet most existing approaches rely on transcriptomic information alone, limiting their ability to capture the regulatory processes underlying cell-state transitions. This work presents ATLAS (Advanced Trajectory Learning from multi-omics At Single-cell resolution), a scverse-compatible framework for trajectory inference in paired single-cell RNA-seq and ATAC-seq data. ATLAS integrates transcriptomic and chromatin accessibility information through Weighted Nearest Neighbor graphs, enabling both molecular layers to jointly inform pseudotime estimation, terminal-state identification, and fate probability inference within a unified multi-omic representation. Across synthetic and real datasets, ATLAS reconstructs coherent developmental trajectories, captures progressive fate commitment, and resolves biologically meaningful lineage structures, demonstrating the effectiveness of multi-omic integration for characterizing cellular dynamics. In addition, ATLAS enables the joint exploration of transcription factor expression and target gene activity along pseudotime, providing direct access to regulatory programs and chromatin-associated transitions that are not detectable from transcriptomic data alone. Overall, ATLAS provides a scalable and biologically informative framework for studying dynamic cellular processes in single-cell multi-omics experiments.