tidyCoverage

tidyCoverage provides a framework for investigating genomic tracks over features, extending the SummarizedExperiment class to facilitate extraction, aggregation, and visualization of coverage data.

Key Features:

• CoverageExperiment class: A data structure extending SummarizedExperiment for storing genomic coverage track data across genomic loci.
• AggregatedCoverage class: A data structure extending SummarizedExperiment for storing aggregated coverage profiles over sets of genomic loci.
• Tidy data manipulation: Relies on tidy data principles for intuitive investigation of collections of genomic tracks over genomic features.
• Extraction and manipulation: Facilitates extraction and manipulation of genomic coverage track data across individual or multiple sets of thousands of genomic loci.
• Visualization: Enables rapid visualization of track coverage at individual genomic loci or aggregated coverage profiles over sets of genomic loci.
• Bioconductor integration: Seamlessly combines with the existing Bioconductor ecosystem to accelerate integration of genome-wide track data in epigenomic analysis workflows.

Scientific Applications:

• Epigenomic analysis: Integration of genome-wide track data in epigenomic analysis workflows.
• Genome-wide data exploration: Principled approach to exploring genome-wide coverage data across genomic features.
• Coverage profile aggregation: Aggregation of coverage profiles over sets of genomic loci for comparative analysis.

Methodology:

tidyCoverage defines CoverageExperiment and AggregatedCoverage classes directly extending the SummarizedExperiment fundamental class, relying on the principle of tidy data manipulation for extraction, aggregation, and visualization of genomic coverage data.