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DOI: 10.1093/bioinformatics/bts485
¤ OpenAccess: Bronze
This work has “Bronze” OA status. This means it is free to read on the publisher landing page, but without any identifiable license.

An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection

Wang Xingbin,Dongwan Kang,Kui Shen,Chi Song,Shuya Lu,Lun‐Ching Chang,Serena G. Liao,Zhiguang Huo,Shaowu Tang,Ying Ding,Naftali Kaminski,Etienne Sibille,Yan Lin,Jia Li,George C. Tseng

Suite
Computer science
Pipeline (software)
2012
Abstract Summary: With the rapid advances and prevalence of high-throughput genomic technologies, integrating information of multiple relevant genomic studies has brought new challenges. Microarray meta-analysis has become a frequently used tool in biomedical research. Little effort, however, has been made to develop a systematic pipeline and user-friendly software. In this article, we present MetaOmics, a suite of three R packages MetaQC, MetaDE and MetaPath, for quality control, differentially expressed gene identification and enriched pathway detection for microarray meta-analysis. MetaQC provides a quantitative and objective tool to assist study inclusion/exclusion criteria for meta-analysis. MetaDE and MetaPath were developed for candidate marker and pathway detection, which provide choices of marker detection, meta-analysis and pathway analysis methods. The system allows flexible input of experimental data, clinical outcome (case–control, multi-class, continuous or survival) and pathway databases. It allows missing values in experimental data and utilizes multi-core parallel computing for fast implementation. It generates informative summary output and visualization plots, operates on different operation systems and can be expanded to include new algorithms or combine different types of genomic data. This software suite provides a comprehensive tool to conveniently implement and compare various genomic meta-analysis pipelines. Availability: http://www.biostat.pitt.edu/bioinfo/software.htm Contact: ctseng@pitt.edu Supplementary Information: Supplementary data are available at Bioinformatics online.
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    An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection” is a paper by Wang Xingbin Dongwan Kang Kui Shen Chi Song Shuya Lu Lun‐Ching Chang Serena G. Liao Zhiguang Huo Shaowu Tang Ying Ding Naftali Kaminski Etienne Sibille Yan Lin Jia Li George C. Tseng published in 2012. It has an Open Access status of “bronze”. You can read and download a PDF Full Text of this paper here.