We aimed to create an extensible framework for single-cell chromatin data analysis that builds on existing tools used in the single-cell, genomics and R language communities. We designed an R toolkit for analysis and visualization of single-cell chromatin data in a way that allowed interoperability with the Seurat R package, designed for the analysis of multimodal single-cell data40-42. The Seurat package uses the Seurat object as its central data structure. The Seurat object is composed of any number of Assay objects containing data for single cells. The Assay object was originally designed for analysis of single-cell gene expression data and allows for storage and retrieval of raw and processed single-cell measurements and metadata associated with each measured feature. To facilitate the analysis of single-cell chromatin data within the Seurat framework, we developed a specialized ‘ChromatinAssay’ object class (Fig. 1b). The ChromatinAssay allows for the storage and retrieval of information needed for the analysis of single-cell chromatin data, including genomic ranges associated with each feature in the experiment, gene annotations, genome build information, DNA motif information and on-disk storage of single-cell
