RankProd 2.0：一个用于在分子谱数据集检测差异表达特征的重构生物导体包。
RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets.
作者信息
Del Carratore Francesco, Jankevics Andris, Eisinga Rob, Heskes Tom, Hong Fangxin, Breitling Rainer
机构信息
Faculty of Science and Engineering, Manchester Institute of Biotechnology, University of Manchester, Manchester M1?7DN, UK.
Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool L69?3GJ, UK.
出版信息
Bioinformatics. 2017 Sep 1;33(17):2774-2775. doi: 10.1093/bioinformatics/btx292.
MOTIVATION
The Rank Product (RP) is a statistical technique widely used to detect differentially expressed features in molecular profiling experiments such as transcriptomics, metabolomics and proteomics studies. An implementation of the RP and the closely related Rank Sum (RS) statistics has been available in the RankProd Bioconductor package for several years. However, several recent advances in the understanding of the statistical foundations of the method have made a complete refactoring of the existing package desirable.
RESULTS
We implemented a completely refactored version of the RankProd package, which provides a more principled implementation of the statistics for unpaired datasets. Moreover, the permutation-based P -value estimation methods have been replaced by exact methods, providing faster and more accurate results.
AVAILABILITY AND IMPLEMENTATION
RankProd 2.0 is available at Bioconductor ( https://www.bioconductor.org/packages/devel/bioc/html/RankProd.html ) and as part of the mzMatch pipeline ( http://www.mzmatch.sourceforge.net ).
CONTACT
rainer.breitling@manchester.ac.uk.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
秩积（RP）是一种统计技术，广泛用于在转录组学、代谢组学和蛋白质组学研究等分子谱实验中检测差异表达特征。秩积生物导体软件包中已经有秩积（RP）和密切相关的秩和（RS）统计量的实现方法好几年了。然而，最近在该方法的统计基础理解方面取得的一些进展使得对现有软件包进行全面重构成为必要。
结果
我们实现了秩积软件包的一个完全重构版本，它为未配对数据集的统计提供了更有原则的实现方法。此外，基于排列的P值估计方法已被精确方法所取代，从而提供了更快、更准确的结果。
可用性和实现
秩积2.0可在生物导体（https://www.bioconductor.org/packages/devel/bioc/html/RankProd.html ）获取，也作为mzMatch管道（http://www.mzmatch.sourceforge.net ）的一部分。
联系方式
rainer.breitling@manchester.ac.uk。
补充信息
补充数据可在《生物信息学》在线获取。
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