Software

  • NIMROD

    We have written a specific program called NIMROD for estimating parameter of ODE based population models. We have adapted the program for parallel computing, in collaboration with the MCIA (Mésocentre de calcul intensif Aquitain) facility, which makes available a large computer with more than 3000 cores.

  • R package marqLevAlg

    An R package for function optimization. Available on CRAN, this package performs a minimization of function based on the Marquardt-Levenberg algorithm. This package is really useful when the surface to optimize is non-strictly convex or far from a quadratic function. A new convergence criterion, the relative distance to maximum (RDM), allows the user to have a better confidence in the stopping points, other than basic algorithm stabilization.

  • R package VSURF

    An R package for Variable Selection Using Random Forests. Available on CRAN, this package performs an automatic (meaning completely data-driven) variable selection procedure. Originally designed to deal with high dimensional data, it can also be applied to standard datasets.

  • R package TcGSA

    An R package for the gene set analysis of longitudinal gene expression data sets. This package implements a Time-course Gene Set Analysis method and provides useful plotting functions facilitating the interpretation of the results.

  • R package R2GUESS

    R2GUESS package is a wrapper of the GUESS (Graphical processing Unit Evolutionary Stochastic Search ) program. GUESS is a 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. The program uses packages from the GNU Scientific Library (GSL) and offers the possibility to re-route computationally intensive linear algebra operations
    towards the Graphical Processing Unit (GPU) through the use of proprietary CULA-dense library.

  • R package sgPLS

    The Sparse Group Partial Least Square package (sgPLS) provides sparse, group, and sparse group versions of partial least square regression models.

  • R package NPflow

    Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data.

  • R package clogitLasso

    Regression Models for matched case-control and case-crossover studies.