BGX - Flexible Bayesian clustering and partition models for gene expression data
Thin Line

Software

CGHmix
Software for detecting copy number changes in CGH experiments (Broët and Richardson)
PoGO
Software for finding statistically over-represented Gene Ontology groups in microarray experiments (Lewin and Grieve)
R Code
R code for the paper: Statistical tools for synthesizing lists of differentially expressed features in microarray experiments, Blangiardo and Richardson

Nmix
Program for Bayesian analysis of univariate normal mixtures by MCMC, implementing the approach of Richardson and Green, Journal of the Royal Statistical Society, B, 59, 731-792 (1997).

Written in Fortran and C.

Gmix
Program for Bayesian analysis of univariate normal mixtures, in which one component has a fixed mean and possible fixed variance, used in the submitted paper "A model-based approach for detecting distinctive gene expression profiles in multiclass response microarray experiments", Broët, P., Richardson, S., Lewin, A., Dalmasso, C. and Magdelenat, H. (2004). Developed from the program (Nmix) for Bayesian analysis of univariate normal mixtures by MCMC, implementing the approach of Richardson and Green, Journal of the Royal Statistical Society, B, 59, 731-792 (1997).

Written in Fortran and C.

BGX
Program for calculating the Bayesian Gene eXpression measure, BGX, for Affymetrix GeneChip arrays. Described in the paper "BGX: a fully Bayesian gene expression index for Affymetrix GeneChip data", Hein, A.-M.K., Richardson, S., Causton, H.C., Ambler, G.K. and Green, P.J. (2004).

Written in C++ and C.
New version (more running options, additional R code for analyzing output)
Old version

BayesDE
WinBUGS code for Bayesian differential expession. Described in the paper "Bayesian Modelling of Differential Gene Expression" (Biometrics, in press), Lewin, A., Richardson, S., Marshall, C., Glazier, A. and Aitman, T. (2005).


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