recoup: flexible and versatile signal visualization from next generation sequencing.
recoup: flexible and versatile signal visualization from next generation sequencing.
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DOI：
10.1186/s12859-020-03902-x
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发表时间：
2021-01-06
影响因子：
3
通讯作者：
Moulos P
中科院分区：
文献类型：
--
作者：
Moulos P
新的基因组测序方案的不断出现以及由此产生的越来越大的数据集的不断产生，继续挑战着对为回答重要的定性和定量生物学问题而产生的潜在信号的有意义的总结和可视化。因此，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型软件的需求正在迅速重新出现。 recoup是一个Bioconductor软件包，用于快速、灵活、多功能和准确地可视化从下一代测序数据生成的基因组覆盖图谱。再加上一个预先计算的多个生物体的基因组区域的数据库，recoup提供了快速，高效和多层次的数据查询处理机制，以最小的努力，同时创建出版质量的可视化。特别关注绘图的可重用性，再现性和实时探索和格式化选项，这些操作很少在类似的可视化工具中得到支持。使用多个定性用户指标评估了补偿，发现它可以平衡重要包功能（包括速度、可视化质量、整体友好性和结果的可重用性）之间的权衡，只需最少的额外计算。 虽然用于NGS数据信号的全面可视化的一些现有解决方案提供了令人满意的结果，但是它们通常在诸如在共同计算环境下毫不费力地跟踪处理和制备步骤、可视化质量和用户友好性的问题上受到损害。recoup是一个独特的软件包，在保持快速和友好的同时，对评估标准的组合进行了平衡的权衡。
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.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
5.8
作者：
Gu, Zuguang;Eils, Roland;Schlesner, Matthias
通讯作者：
Schlesner, Matthias
影响因子：
4.4
作者：
Shen L;Shao N;Liu X;Nestler E
通讯作者：
Nestler E
影响因子：
2.7
作者：
Georgiou, Georgios;van Heeringen, Simon J.
通讯作者：
van Heeringen, Simon J.
单细胞染色质可及性揭示了调节变化的原理。
影响因子：
64.8
作者：
Buenrostro JD;Wu B;Litzenburger UM;Ruff D;Gonzales ML;Snyder MP;Chang HY;Greenleaf WJ
通讯作者：
Greenleaf WJ