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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/25171

Title: IsoGeneGUI: Multiple Approaches for Dose-Response Analysis of Microarray Data Using R
Authors: Otava, Martin
Sengupta, Rudradev
Shkedy, Ziv
Lin, Dan
Pramana, Setia
Verbeke, Tobias
Haldermans, Philippe
Hothorn, Ludwig A.
Gerhard, Daniel
Kuiper, Rebecca M.
Klinglmueller, Florian
Kasim, Adetayo
Issue Date: 2017
Citation: The R journal, 9(1), p. 14-26
Abstract: The analysis of transcriptomic experiments with ordered covariates, such as dose-response data, has become a central topic in bioinformatics, in particular in omics studies. Consequently, multiple R packages on CRAN and Bioconductor are designed to analyse microarray data from various perspectives under the assumption of order restriction. We introduce the new R package IsoGene Graphical User Interface (IsoGeneGUI), an extension of the original IsoGene package that includes methods from most of available R packages designed for the analysis of order restricted microarray data, namely orQA, ORIClust, goric and ORCME. The methods included in the new IsoGeneGUI range from inference and estimation to model selection and clustering tools. The IsoGeneGUI is not only the most complete tool for the analysis of order restricted microarray experiments available in R but also it can be used to analyse other types of dose-response data. The package provides all the methods in a user friendly fashion, so analyses can be implemented by users with limited knowledge of R programming.
URI: http://hdl.handle.net/1942/25171
Link to publication: https://journal.r-project.org/archive/2017/RJ-2017-002/RJ-2017-002.pdf
ISSN: 2073-4859
Category: A1
Type: Journal Contribution
Appears in Collections: Research publications

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