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.
Highlights
Modelling the dose-response relationship plays an important role in the drug discovery process in the pharmaceutical industry
Order restriction is often assumed in the dose-response modelling, usually in terms of monotone trend (Lin et al, 2012b)
Methods for inference, estimation, clustering and model selection available in IsoGeneGUI package are introduced in following section
Summary
Modelling the dose-response relationship plays an important role in the drug discovery process in the pharmaceutical industry. The R packages IsoGene (Lin et al, 2013 and Pramana et al, 2010) and orQA (Klinglmueller, 2010) were developed for inference, goric (Gerhard and Kuiper, 2012 and Kuiper and Hoijtink, 2013) for model selection, and ORCME (Kasim et al, 2014) and ORIClust (Liu et al, 2012) were developed for order restricted clustering of genes. In addition to the data analysis tools for estimation, inference, model selection and clustering, the package contains many tools for exporting results, their visualization and easy handling of produced figures.
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