Journal Article

tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation

Antoine Chambaz and Pierre Neuvial

in Bioinformatics

Volume 31, issue 18, pages 3054-3056
Published in print September 2015 | ISSN: 1367-4803
Published online May 2015 | e-ISSN: 1460-2059 | DOI: https://dx.doi.org/10.1093/bioinformatics/btv320
tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation

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Summary: We describe the implementation of the method introduced by Chambaz et al. in 2012. We also demonstrate its genome-wide application to the integrative search of new regions with strong association between DNA copy number and gene expression accounting for DNA methylation in breast cancers.

Availability and implementation: An open-source R package tmle.npvi is available from CRAN (http://cran.r-project.org/).

Contact: pierre.neuvial@genopole.cnrs.fr

Journal Article.  1439 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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