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Single-cell ATAC+RNA linking (SCARlink) uses multi-omic single-cell ATAC and RNA to 1. predict gene expression from chromatin accessibility and 2. predict regulatory regions for each gene in a cell-type-specific manner. It takes preprocessed scRNA-seq and scATAC-seq in Seurat and ArchR objects respectively. Preprocessing details are provided in example notebook. Tutorial notebook describes how to run SCARlink on a small example dataset.

Paper: Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis by Mitra, S et al., 2024: https://www.nature.com/articles/s41588-024-01689-8.