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IntegrOmics: an R package to unravel relationships between two omics datasets.


ABSTRACT:

Motivation

With the availability of many 'omics' data, such as transcriptomics, proteomics or metabolomics, the integrative or joint analysis of multiple datasets from different technology platforms is becoming crucial to unravel the relationships between different biological functional levels. However, the development of such an analysis is a major computational and technical challenge as most approaches suffer from high data dimensionality. New methodologies need to be developed and validated.

Results

integrOmics efficiently performs integrative analyses of two types of 'omics' variables that are measured on the same samples. It includes a regularized version of canonical correlation analysis to enlighten correlations between two datasets, and a sparse version of partial least squares (PLS) regression that includes simultaneous variable selection in both datasets. The usefulness of both approaches has been demonstrated previously and successfully applied in various integrative studies.

Availability

integrOmics is freely available from http://CRAN.R-project.org/ or from the web site companion (http://math.univ-toulouse.fr/biostat) that provides full documentation and tutorials.

Contact

k.lecao@uq.edu.au

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Le Cao KA 

PROVIDER: S-EPMC2781751 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature

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Publications

integrOmics: an R package to unravel relationships between two omics datasets.

Lê Cao Kim-Anh KA   González Ignacio I   Déjean Sébastien S  

Bioinformatics (Oxford, England) 20090825 21


<h4>Motivation</h4>With the availability of many 'omics' data, such as transcriptomics, proteomics or metabolomics, the integrative or joint analysis of multiple datasets from different technology platforms is becoming crucial to unravel the relationships between different biological functional levels. However, the development of such an analysis is a major computational and technical challenge as most approaches suffer from high data dimensionality. New methodologies need to be developed and va  ...[more]

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