Epigenomics coverage data extraction and aggregation in R with tidyCoverage

Abstract

Abstract Summary The tidyCoverage R package provides a framework for intuitive investigation of collections of genomic tracks over genomic features, relying on the principle of tidy data manipulation. It defines two data structures, CoverageExperiment and AggregatedCoverage classes, directly extending the SummarizedExperiment fundamental class, and introduces a principled approach to exploring genome-wide data. This infrastructure facilitates the extraction and manipulation of genomic coverage track data across individual or multiple sets of thousands of genomic loci. This allows the end user to rapidly visualize track coverage at individual genomic loci or aggregated coverage profiles over sets of genomic loci. tidyCoverage seamlessly combines with the existing Bioconductor ecosystem to accelerate the integration of genome-wide track data in epigenomic analysis workflows. tidyCoverage emerges as a valuable tool, contributing to the advancement of epigenomics research by promoting consistency, reproducibility, and accessibility in data analysis. Availability and implementation tidyCoverage is an R package freely available from Bioconductor ≥ 3.19 (https://www.bioconductor.org/packages/tidyCoverage) for R ≥ 4.4. The software is distributed under the MIT License and is accompanied by example files and data.