RJ-2017-002.knit

title: ‘IsoGeneGUI: Multiple Approaches for Dose-Response Analysis of Microarray Data Using R’ description: 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. author: - Martin Otava - Rudradev Sengupta - Ziv Shkedy - Dan Lin - Setia Pramana - Tobias Verbeke - Philippe Haldermans - Ludwig A. Hothorn - Daniel Gerhard - Rebecca M. Kuiper - Florian Klinglmueller - ’ Adetayo Kasim’ date: ‘2017-05-10’ date_received: ‘2015-07-22’ journal: title: The R Journal issn: 2073-4859 firstpage: 14 lastpage: 26 volume: 9 issue: 1 slug: RJ-2017-002 packages: cran: - IsoGene - orQA - goric - ORCME - ORIClust - limma - mratios bioc: ~ preview: preview.png CTV: Cluster output: distill::distill_article: self_contained: no toc: no legacy_pdf: yes pdf_url: RJ-2017-002.pdf citation_url: https://doi.org/10.32614/RJ-2017-002 doi: 10.32614/RJ-2017-002 creative_commons: CC BY csl: /home/mitchell/R/x86_64-pc-linux-gnu-library/4.1/rjtools/rjournal.csl

CRAN packages used

IsoGene, orQA, goric, ORCME, ORIClust, limma, mratios

CRAN Task Views implied by cited packages

Cluster

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Citation

For attribution, please cite this work as

Otava, et al., "IsoGeneGUI: Multiple Approaches for Dose-Response Analysis of Microarray Data Using R", The R Journal, 2017

BibTeX citation

@article{RJ-2017-002,
  author = {Otava, Martin and Sengupta, Rudradev and Shkedy, Ziv and Lin, Dan and Pramana, Setia and Verbeke, Tobias and Haldermans, Philippe and Hothorn, Ludwig A. and Gerhard, Daniel and Kuiper, Rebecca M. and Klinglmueller, Florian and Kasim,  Adetayo},
  title = {IsoGeneGUI: Multiple Approaches for Dose-Response Analysis of Microarray Data Using R},
  journal = {The R Journal},
  year = {2017},
  note = {https://doi.org/10.32614/RJ-2017-002},
  doi = {10.32614/RJ-2017-002},
  volume = {9},
  issue = {1},
  issn = {2073-4859},
  pages = {14-26}
}