Software

QTL lasso R function

QTL lasso.

Profile regression adjusting for confounders and withoutadjusting for confounders

Software and documentation for examining the joint effect of multiple risk factors using exposure risk profiles.

BATMAN

R package for deconvolving resonance peaks from NMR spectra and obtaining concentration estimates for the corresponding metabolites automatically. Parallel processing is available if processing several spectra.

GUESS

Computationally optimised C++ implementation of a fully Bayesian variable selection approach that can analyse, in a genome-wide context, single and multiple responses in an integrated way.

ESS++

Software and documentation for a fully Bayesian variable selection approach for single and multiple response linear regression, using evolutionary Monte Carlo.

MMSEQ

Software and instructions for fast, scalable isoform expression estimation using multi-mapping RNA-seq reads.

MMBGX

Software and instructions for multi-mapping Bayesian analysis of whole-transcript Affymetrix expression arrays.

BVS

MATLAB toolbox for binary Bayesian variable selection (logistic and probit regression) suitable for high-dimensional data, including block MCMC samplers and a parallel tempering algorithm to speed up the sampling process.

Blangiardo & Richardson 2007 WinBUGS code

A Bayesian calibration model for combining different pre-processing methods in Affymetrix chips

BGX

Bioconductor R package and standalone program for calculating the Bayesian Gene eXpression measure, BGX, for Affymetrix GeneChip arrays.

BGmix

R package for Bayesian hierarchical mixture models for differential gene expression (Lewin, Bochkina and Richardson). This package will soon be available on Bioconductor. Until then, here is the source code(WinZip works on this file).

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)

BGcom

R package for finding lists of features commonly perturbed in 2 or more experiments as described in Blangiardo and Richardson "Statistical tools for synthesizing lists of differentially expressed features in related experiments", Genome Biology, 8, R54

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.

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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