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Abstract Emerging single-cell sequencing protocols allow researchers to study multiple layers of epigenetic regulation while resolving tissue heterogeneity. However, despite the rising popularity of such single-cell epigenomics assays, the lack of easy-to-use computational tools that allow flexible quality control and data exploration hinders their broad adoption. We introduce the Single-Cell Informatics ( sincei ) toolkit. sincei provides an easy-to-use, command-line interface for the exploration of data from a wide range of single-cell (epi)genomics protocols directly from aligned reads stored in .bam files. sincei can be installed via bioconda and the documentation is available at https://sincei.readthedocs.io .
Bhardwaj et al. (Mon,) studied this question.