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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/24316

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: 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.
Notes: [Otava, Martin; Sengupta, Rudradev; Shkedy, Ziv; Lin, Dan] Univ Hasselt, Interuniv Inst Biostat & Stat Bioinformat, Martelarenlaan 32, B-3500 Hasselt, Belgium. [Lin, Dan] GlaxoSmithKline, Rue Inst 89, B-1330 Rixensart, Belgium. [Pramana, Setia] Sekolah Tinggi Ilmu Stat, Inst Stat, Jl Otto Iskandardinata 64C, Jakarta 13330, Indonesia. [Pramana, Setia] Karolinska Inst, Dept Med Epidemiol & Biostat, POB 281, SE-17177 Stockholm, Sweden. [Verbeke, Tobias] Open Analyt NV, Jupiterstr 20, B-2600 Antwerp, Belgium. [Haldermans, Philippe] PXL Univ Coll, PXL IT, Elfde Liniestr 24, B-3500 Hasselt, Belgium. [Hothorn, Ludwig A.] Leibniz Univ Hannover, Inst Biostat, Herrenhaeuserstr 2, D-30419 Hannover, Germany. [Gerhard, Daniel] Univ Canterbury, Sch Math & Stat, Private Bag 4800, Christchurch 8140, New Zealand. [Kuiper, Rebecca M.] Univ Utrecht, Dept Methodol & Stat, Padualaan 14, NL-3584 CH Utrecht, Netherlands. [Klinglmueller, Florian] Med Univ Vienna, Ctr Med Stat & Informat, Sect Med Stat, Spitalgasse 23, A-1090 Vienna, Austria. [Kasim, Adetayo] Univ Durham, Wolfson Res Inst Hlth & Wellbeing, Queens Campus,Univ Blvd, Stockton On Tees TS17 6BH, England.
URI: http://hdl.handle.net/1942/24316
Link to publication: https://journal.r-project.org/archive/2017/RJ-2017-002/RJ-2017-002.pdf
ISI #: 000404756200003
ISSN: 2073-4859
Category: A1
Type: Journal Contribution
Validation: ecoom, 2018
Appears in Collections: Research publications

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