IsoGeneGUI: Multiple Approaches for Dose-Response Analysis of Microarray Data Using R (2017)
AuthorsOtava M, Sengupta R, Shkedy Z, Lin D, Pramana S, Verbeke T, Haldermans P, Hothorn LA, Gerhard D, Kuiper RM, Klinglmueller F, Kasim Ashow all
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.
CitationOtava M, Sengupta R, Shkedy Z, Lin D, Pramana S, Verbeke T, Haldermans P, Hothorn LA, Gerhard D, Kuiper RM, Klinglmueller F, Kasim A (2017). IsoGeneGUI: Multiple Approaches for Dose-Response Analysis of Microarray Data Using R. The R Journal.
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ANZSRC Fields of Research06 - Biological Sciences::0604 - Genetics::060405 - Gene Expression (incl. Microarray and other genome-wide approaches)
06 - Biological Sciences::0601 - Biochemistry and Cell Biology::060102 - Bioinformatics
08 - Information and Computing Sciences::0803 - Computer Software::080301 - Bioinformatics Software