csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows.
csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows.
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DOI：
10.1093/nar/gkv1191
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发表时间：
2016-03-18
影响因子：
14.9
通讯作者：
Smyth GK
中科院分区：
文献类型：
--
作者：
Lun AT;Smyth GK
染色质免疫沉淀与大规模平行测序（ChIP-seq）被广泛用于鉴定基因组中靶蛋白的结合位点。一个重要的科学应用是鉴定不同处理条件之间蛋白质结合的变化，即检测差异结合。这可以揭示结合变化可能有助于治疗效果的潜在机制。csaw软件包提供了一个框架，从头检测差异结合的基因组区域。它使用基于窗口的策略来总结整个基因组的读段计数。它利用现有的统计软件来测试每个窗口中的显著差异。最后，它将窗口聚类为区域以供输出，并在所有检测到的区域上适当地控制错误发现率。csaw软件包可以处理任意复杂的涉及生物复制的实验设计。它可以应用于转录因子和组蛋白标记数据集，并且更一般地，应用于测量基因组覆盖率的任何类型的测序数据。csaw对模拟和真实的数据的从头DB分析优于现有方法。csaw作为R软件包实现，可从开源Bioconductor项目免费获得。
Chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) is widely used to identify binding sites for a target protein in the genome. An important scientific application is to identify changes in protein binding between different treatment conditions, i.e. to detect differential binding. This can reveal potential mechanisms through which changes in binding may contribute to the treatment effect. The csaw package provides a framework for the de novo detection of differentially bound genomic regions. It uses a window-based strategy to summarize read counts across the genome. It exploits existing statistical software to test for significant differences in each window. Finally, it clusters windows into regions for output and controls the false discovery rate properly over all detected regions. The csaw package can handle arbitrarily complex experimental designs involving biological replicates. It can be applied to both transcription factor and histone mark datasets, and, more generally, to any type of sequencing data measuring genomic coverage. csaw performs favorably against existing methods for de novo DB analyses on both simulated and real data. csaw is implemented as a R software package and is freely available from the open-source Bioconductor project.