RankProd 2.0: A refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets
Publication year
2017Number of pages
2 p.
Source
Bioinformatics, 33, 17, (2017), pp. 2774-2775ISSN
Publication type
Article / Letter to editor

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Organization
SW OZ RSCR SOC
Data Science
Journal title
Bioinformatics
Volume
vol. 33
Issue
iss. 17
Languages used
English (eng)
Page start
p. 2774
Page end
p. 2775
Subject
Data Science; Inequality, cohesion and modernization; Ongelijkheid, cohesie en moderniseringAbstract
Motivation: The Rank Products 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 Rank Product (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 Moreover, the permutation-based p-value estimation methods have been replaced by exact methods, providing faster and more accurate results.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: 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).
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- Academic publications [203587]
- Electronic publications [101944]
- Faculty of Science [32092]
- Faculty of Social Sciences [27277]
- Open Access publications [70663]
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