regioneR：一个用于基于排列检验进行基因组区域关联分析的R/Bioconductor软件包。
regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.
作者信息
Gel Bernat, Díez-Villanueva Anna, Serra Eduard, Buschbeck Marcus, Peinado Miguel A, Malinverni Roberto
机构信息
Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain and.
Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain and Josep Carreras Institute for Leukaemia Research (IJC), Campus ICO-HGTP, Campus Can Ruti, Badalona, Spain.
出版信息
Bioinformatics. 2016 Jan 15;32(2):289-91. doi: 10.1093/bioinformatics/btv562. Epub 2015 Sep 30.
MOTIVATION
Statistically assessing the relation between a set of genomic regions and other genomic features is a common challenging task in genomic and epigenomic analyses. Randomization based approaches implicitly take into account the complexity of the genome without the need of assuming an underlying statistical model.
SUMMARY
regioneR is an R package that implements a permutation test framework specifically designed to work with genomic regions. In addition to the predefined randomization and evaluation strategies, regioneR is fully customizable allowing the use of custom strategies to adapt it to specific questions. Finally, it also implements a novel function to evaluate the local specificity of the detected association.
AVAILABILITY AND IMPLEMENTATION
regioneR is an R package released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/regioneR).
CONTACT
动机
在基因组和表观基因组分析中，从统计学角度评估一组基因组区域与其他基因组特征之间的关系是一项常见的具有挑战性的任务。基于随机化的方法隐含地考虑了基因组的复杂性，而无需假设潜在的统计模型。
总结
regioneR是一个R包，它实现了一个专门设计用于处理基因组区域的置换检验框架。除了预定义的随机化和评估策略外，regioneR完全可定制，允许使用自定义策略使其适应特定问题。最后，它还实现了一个新功能来评估检测到的关联的局部特异性。
可用性和实现
regioneR是一个根据Artistic-2.0许可发布的R包。源代码和文档可通过Bioconductor（http://www.bioconductor.org/packages/regioneR）免费获取。
联系方式
Zotero 插件