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sincei provides a flexible, easy-to-use command-line interface and python API to work with single-cell epigenomics data directly from BAM files. It can:
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- Aggregate signal in bins, genes or any feature of interest from single-cells.
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- Perform read-level and count-level quality control.
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- Perform dimensionality reduction and clustering of various types of single-cell data (open chromatin, histone marks, methylation etc..).
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- Create coverage files (bigwigs) for visualization.
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