Cisformer Documentation
Cisformer is a Transformer-based framework for cross-modality generation and regulatory inference in single-cell RNA-seq and single-cell ATAC-seq data. It supports RNA-to-ATAC prediction, ATAC-to-RNA prediction, and cell-type-specific cCRE-gene link inference from trained ATAC-to-RNA models.
Version 1.1.0 adds mouse reference support, species-aware config generation, automatic ATAC-to-RNA log1p detection, and faster link matrix generation.