regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.
regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.
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DOI：
10.1093/bioinformatics/btv562
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发表时间：
2016-01-15
期刊：
影响因子：
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通讯作者：
Malinverni R
中科院分区：
文献类型：
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作者：
Gel B;Díez-Villanueva A;Serra E;Buschbeck M;Peinado MA;Malinverni R
动机：统计评估一组基因组区域和其他基因组特征之间的关系是基因组和表观基因组分析中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，而不需要假设基础统计模型。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排列测试框架。除了预定义的随机化和评估策略外，regioneR还可以完全自定义，允许使用自定义策略来适应特定问题。最后，它还实现了一个新的功能来评估检测到的关联的局部特异性。可用性和实现：regioneR是在Artistic-2.0许可证下发布的R软件包。源代码和文件可通过Bioconductor（http：//www.bioconductor.org/packages/regioneR）免费获取。联系方式：rmalinverni@carrerasresearch.org
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: rmalinverni@carrerasresearch.org