Section: Software

SMVar

Participant : Guillemette Marot.

SMVar is a specialised software for microarrays. This R package implements the structural model for variances in order to detect differentially expressed genes from gene expression data. It performs gene expression differential analysis, based on a particular variance modelling. Its main competitor is the Bioconductor R package limma but limma assumes a common variance between the two groups to be compared while SMVar relaxes this assumption.

Guillemette Marot is the main contributor and the maintainer of this packages and spent around one year full time for this package between the conception, the implementation, and the documentation. Her PhD advisors (Florence Jaffrézic, Claus-Dieter Mayer, Jean-Louis Foulley) helped her with the conception but she implemented alone the code. She received some help from Anne de la Foye (INRA, Clermont-Ferrand) to correct the bugs in the first versions.

First versions have been posted to the CRAN, the official website of the R software, in 2009. New versions for this package were released in August 2011 in order to take into account remarks from the main users (biologists or biostatisticians analysing gene expression data). This software is routinely used by biologists from INRA, Jouy en Josas (it has been included in a local analysis pipeline) but its diffusion on the CRAN makes it available to a wider community, as attested by the publications citing the software(F. Jaffrézic, G. Marot, S. Degrelle, I. Hue, J.-L. Foulley. A structural mixed model for variances in differential gene expression studies, in "Genetical Research", 2007, vol. 89, no 1, p. 19–-25.).

More information on the website http://cran.r-project.org/web/packages/SMVar/index.html