SnapATAC

SnapATAC analyzes single-cell and single-nucleus ATAC-seq (scATAC-seq) datasets to identify cis-regulatory elements and infer cell-type-specific transcriptional regulators for dissecting cellular heterogeneity.

Key Features:

• scATAC-seq and single-nucleus ATAC-seq support: Processes single-cell ATAC-seq and single-nucleus ATAC-seq datasets to analyze chromatin accessibility.
• Nyström method scalability: Uses the Nyström method to scale analyses to datasets comprising up to a million cells.
• Noise and heterogeneity handling: Addresses high noise levels and sample heterogeneity inherent in open chromatin assays.
• Cis-regulatory element identification: Identifies cis-regulatory elements that control cell-type-specific gene expression patterns.
• Transcriptional regulator inference: Infers candidate cell-type-specific transcriptional regulators from accessibility profiles.
• Unbiased cellular heterogeneity dissection: Performs unbiased dissection of cellular heterogeneity to resolve distinct cell populations.
• Cellular state trajectory mapping: Maps cellular state trajectories from accessibility data.
• Integration of computational tools: Integrates existing computational tools into a comprehensive analysis package.

Scientific Applications:

• Large-scale chromatin accessibility profiling: Applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex, identifying approximately 370,000 candidate regulatory elements across 31 distinct cell populations.
• Cell-type regulatory inference: Enables discovery of cell-type-specific regulatory elements and candidate transcriptional regulators underlying gene expression programs.

Methodology:

Uses the Nyström method for scalable analysis, performs unbiased dissection of cellular heterogeneity and mapping of cellular state trajectories, and integrates existing computational tools into a comprehensive package.