The relentless continuing emergence of new genomic sequencing protocols and the resulting generation of ever larger datasets continue to challenge the meaningful summarization and visualization of the underlying signal generated to answer important qualitative and quantitative biological questions. As a result, the need for novel software able to reliably produce quick, comprehensive, and easily repeatable genomic signal visualizations in a user-friendly manner is rapidly re-emerging. recoup is a Bioconductor package for quick, flexible, versatile, and accurate visualization of genomic coverage profiles generated from Next Generation Sequencing data. Coupled with a database of precalculated genomic regions for multiple organisms, recoup offers processing mechanisms for quick, efficient, and multi-level data interrogation with minimal effort, while at the same time creating publication-quality visualizations. Special focus is given on plot reusability, reproducibility, and real-time exploration and formatting options, operations rarely supported in similar visualization tools in a profound way. recoup was assessed using several qualitative user metrics and found to balance the tradeoff between important package features, including speed, visualization quality, overall friendliness, and the reusability of the results with minimal additional calculations. While some existing solutions for the comprehensive visualization of NGS data signal offer satisfying results, they are often compromised regarding issues such as effortless tracking of processing and preparation steps under a common computational environment, visualization quality and user friendliness. recoup is a unique package presenting a balanced tradeoff for a combination of assessment criteria while remaining fast and friendly.

中文翻译：

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回收：来自下一代测序的灵活，通用的信号可视化

新基因组测序方案的不断涌现以及由此产生的越来越大的数据集，继续挑战着为回答重要的定性和定量生物学问题而产生的基础信号的有意义的总结和可视化。结果，对能够以用户友好的方式可靠地产生快速，全面且易于重复的基因组信号可视化的新颖软件的需求正在迅速重新出现。recoup是一种Bioconductor软件包，用于快速，灵活，通用和准确地可视化从下一代测序数据生成的基因组覆盖率概况。结合多种生物的预先计算的基因组区域数据库，recoup提供了处理机制，可实现快速，高效和多层次的数据查询，而所需的工作量最小，同时创建发布质量的可视化文件。重点关注地块的可重用性，可重复性以及实时探索和格式化选项，而在类似的可视化工具中很少以深刻的方式支持操作。使用几种定性用户指标评估了可收回性，并发现在重要的软件包功能（包括速度，可视化质量，总体友好性以及结果的可重用性）之间进行权衡，而无需进行额外的最少计算。虽然一些用于NGS数据信号的全面可视化的现有解决方案提供了令人满意的结果，但是它们在诸如通用计算环境下不费力地跟踪处理和准备步骤，可视化质量和用户友好性等问题上经常受到损害。