scROMA: batch-aware pathway-activity inference and a ground-truth simulation framework for single-cell transcriptomics

Batch-aware, SVD-based pathway-activity inference for single-cell transcriptomics, natively integrated with the Scanpy/AnnData ecosystem. scROMA is a Python implementation of ROMA (Representation and Quantification Of Module Activity) that scores each gene set from the coordinated variation among its member genes, with per-cell activity scores, per-gene contributions, and permutation-based significance. Its batch-aware extension corrects technical variation inside the gene-set subspace rather than across the whole transcriptome, and it ships with a generative simulation framework that produces data with fully specified ground-truth pathway activity. Paper version release.