Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris 75015, France.
Bioinformatics. 2024 Aug 2;40(8). doi: 10.1093/bioinformatics/btae487.
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.
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.
tidyCoverage R 包提供了一个直观研究基因组特征上基因组轨迹集合的框架，它依赖于整洁数据操作的原理。它定义了两个数据结构，CoverageExperiment 和 AggregatedCoverage 类，直接扩展了 SummarizedExperiment 基本类，并引入了一种探索全基因组数据的原则方法。该基础架构有助于在单个或多个数千个基因组位置集上提取和操作基因组覆盖轨迹数据。这允许最终用户快速可视化单个基因组位置或基因组位置集上的聚合覆盖分布。tidyCoverage 与现有的 Bioconductor 生态系统无缝结合，加速了全基因组轨迹数据在表观基因组分析工作流程中的集成。tidyCoverage 作为一个有价值的工具出现，通过在数据分析中促进一致性、可重复性和可访问性，为推进表观基因组学研究做出了贡献。
tidyCoverage 是一个 R 包，可从 Bioconductor ≥ 3.19（https://www.bioconductor.org/packages/tidyCoverage）免费获得，适用于 R ≥ 4.4。该软件根据 MIT 许可证分发，并附有示例文件和数据。
