PeakRanger: a cloud-enabled peak caller for ChIP-seq data.
PeakRanger: a cloud-enabled peak caller for ChIP-seq data.
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DOI：
10.1186/1471-2105-12-139
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发表时间：
2011-05-09
影响因子：
3
通讯作者：
Stein L
中科院分区：
文献类型：
--
作者：
Feng X;Grossman R;Stein L
染色质免疫沉淀（CHIP）与大量平行的短阅读测序（SEQ）相结合，用于探测染色质动力学。尽管有许多算法可以从CHIP-SEQ数据集中调用峰值，但大多数算法要么调整以处理点状位点，例如转录因子结合位点或宽区域，例如组蛋白修饰标记；很少有人可以做。其他算法的可配置性，大型数据集的性能以及区分紧密间隔峰的能力受到限制。
在本文中，我们介绍了PeakRanger，这是一个峰呼叫者软件包，在点状和宽阔的站点上同样效果，可以解决紧密的峰值，具有出色的性能，并且可以易于定制。此外，可以在平行的云计算环境中运行峰值，以在非常大的数据集上获得极高的性能。我们提出了一系列基准测试，以评估其他10个峰呼叫者的峰值条件，并在真实和合成数据集中证明了峰值峰的性能。我们还介绍了PeakRanger的真实世界使用情况，包括Modencode项目中的峰值打电话。
与经过测试的其他峰值呼叫者相比，峰式峰在区分极限峰的方面提供了改进的分辨率。在确定结合事件的精确位置方面，PeakRanger具有高于平均水平的空间精度。 PeakRanger在评估的所有基准中也具有出色的灵敏度和特异性。此外，PeakRanger在单个处理器系统上运行时的运行时间可显着改善，并且在允许利用云计算资源提供的MapReduce并行环境时进行了明显的改进。可以在Modencode项目的官方网站上下载PeakRanger：http：//www.modencode.org/software/ranger/
Chromatin immunoprecipitation (ChIP), coupled with massively parallel short-read sequencing (seq) is used to probe chromatin dynamics. Although there are many algorithms to call peaks from ChIP-seq datasets, most are tuned either to handle punctate sites, such as transcriptional factor binding sites, or broad regions, such as histone modification marks; few can do both. Other algorithms are limited in their configurability, performance on large data sets, and ability to distinguish closely-spaced peaks. In this paper, we introduce PeakRanger, a peak caller software package that works equally well on punctate and broad sites, can resolve closely-spaced peaks, has excellent performance, and is easily customized. In addition, PeakRanger can be run in a parallel cloud computing environment to obtain extremely high performance on very large data sets. We present a series of benchmarks to evaluate PeakRanger against 10 other peak callers, and demonstrate the performance of PeakRanger on both real and synthetic data sets. We also present real world usages of PeakRanger, including peak-calling in the modENCODE project. Compared to other peak callers tested, PeakRanger offers improved resolution in distinguishing extremely closely-spaced peaks. PeakRanger has above-average spatial accuracy in terms of identifying the precise location of binding events. PeakRanger also has excellent sensitivity and specificity in all benchmarks evaluated. In addition, PeakRanger offers significant improvements in run time when running on a single processor system, and very marked improvements when allowed to take advantage of the MapReduce parallel environment offered by a cloud computing resource. PeakRanger can be downloaded at the official site of modENCODE project: http://www.modencode.org/software/ranger/
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影响因子：
3
作者：
Nix DA;Courdy SJ;Boucher KM
通讯作者：
Boucher KM
影响因子：
30.8
作者：
He, Housheng Hansen;Meyer, Clifford A.;Shin, Hyunjin;Bailey, Shannon T.;Wei, Gang;Wang, Qianben;Zhang, Yong;Xu, Kexin;Ni, Min;Lupien, Mathieu;Mieczkowski, Piotr;Lieb, Jason D.;Zhao, Keji;Brown, Myles;Liu, X. Shirley
通讯作者：
Liu, X. Shirley
影响因子：
64.8
作者：
Heintzman, Nathaniel D.;Hon, Gary C.;Hawkins, R. David;Kheradpour, Pouya;Stark, Alexander;Harp, Lindsey F.;Ye, Zhen;Lee, Leonard K.;Stuart, Rhona K.;Ching, Christina W.;Ching, Keith A.;Antosiewicz-Bourget, Jessica E.;Liu, Hui;Zhang, Xinmin;Green, Roland D.;Lobanenkov, Victor V.;Stewart, Ron;Thomson, James A.;Crawford, Gregory E.;Kellis, Manolis;Ren, Bing
通讯作者：
Ren, Bing
影响因子：
46.9
作者：
Ji, Hongkai;Jiang, Hui;Ma, Wenxiu;Johnson, David S.;Myers, Richard M.;Wong, Wing H.
通讯作者：
Wong, Wing H.
影响因子：
48
作者：
Pepke, Shirley;Wold, Barbara;Mortazavi, Ali
通讯作者：
Mortazavi, Ali