scATAC-pro

scATAC-pro processes single-cell chromatin accessibility sequencing (scCAS) data to perform preprocessing, quality assessment, peak calling, generation of peak-by-cell count matrices, and downstream analyses including dimension reduction, clustering, differential accessibility, transcription factor motif enrichment, and footprinting.

Key Features:

• Preprocessing Pipeline: Accepts raw fastq files and performs demultiplexing, adaptor trimming, mapping to reference genomes, peak calling, cell calling, signal generation, and quality control to produce a peak-by-cell count matrix.
• Downstream Analysis: Implements dimension reduction, cell clustering, differential accessibility analysis, transcription factor (TF) motif enrichment analysis, and footprinting analysis.
• Quality Assessment: Computes a range of quality control metrics across key experimental steps and generates comprehensive summary reports for quality assessment and downstream analyses.
• Flexibility and Customization: Provides configurable options for analysis modules and curated default parameters that can be adjusted for different datasets.
• Utility Functions: Includes functions to generate input files for a variety of downstream analyses and data visualization workflows.

Scientific Applications:

• Epigenomic Heterogeneity: Enables investigation of epigenomic heterogeneity in complex tissues at single-cell resolution.
• Cellular Differentiation: Facilitates analysis of chromatin accessibility changes underlying cellular differentiation processes.
• Regulatory Network Inference: Supports identification of regulatory mechanisms via TF motif enrichment and footprinting.
• Disease Mechanisms and Translational Research: Applies to studies of healthy and diseased tissues to probe disease mechanisms and translational applications.

Methodology:

Computational modules explicitly include demultiplexing, adaptor trimming, mapping to reference genomes, peak calling, cell calling, signal generation, quality control, peak-by-cell count matrix generation, dimension reduction, clustering, differential accessibility testing, TF motif enrichment, footprinting, QC metric computation, and generation of summary reports, with utility functions to produce input files for downstream analyses.