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IsoGeneGUI : multiple approaches for dose-response analysis of microarray data using R.

Otava, Martin and Sengupta, Rudradev and Shkedy, Ziv and Lin, Dan and Pramana, Setia and Verbeke, Tobias and Haldermans, Philippe and A. Hothorn, Ludwig and Gerhard, Daniel and Kuiper, Rebecca M. and Klinglmueller, Florian and Kasim, Adetayo (2017) 'IsoGeneGUI : multiple approaches for dose-response analysis of microarray data using R.', The R journal., 9 (1). p. 14.


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.

Item Type:Article
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First Live Deposit - 14 July 2017
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Publisher statement:This article is licensed under a Creative Commons Attribution 4.0 International license.
Record Created:14 Jul 2017 12:58
Last Modified:14 Jul 2017 13:26

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