Section: New Software and Platforms

Older software still maintained by SISTM

NIMROD

Normal approximation Inference in Models with Random effects based on Ordinary Differential equations

• Keywords: Biostatistics - Optimization

• Functional Description We have written a specific program called NIMROD for estimating parameter of ODE based population models.

• Contact: Rodolphe Thiebaut

• URL: http://etudes.isped.u-bordeaux2.fr/BIOSTATISTIQUE/NIMROD/documentation/html/index.html

R2GUESS

Graphical processing Unit Evolutionary Stochastic Search

• Keywords: Bioinformatics - Biostatistics

• Functional Description 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.

• Contact: Rodolphe Thiebaut

• URL: https://cran.r-project.org/web/packages/R2GUESS/index.html

TcGSA

Time-course Gene Set Analysis

• Keywords: Bioinformatics - Genomics

• Functional Description An R package for the gene set analysis of longitudinal gene expression data sets. Under development, and soon to be available on the CRAN website, this package implements a Time-course Gene Set Analysis method and provides useful plotting functions facilitating the interpretation of the results.

• Contact: Boris Hejblum

• URL: https://cran.r-project.org/web/packages/TcGSA/index.html

VSURF

Variable Selection Using Random Forests

• Keyword: Bioinformatics

• Functional Description 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.

• Contact: Robin Genuer

• URL: https://cran.r-project.org/web/packages/VSURF/index.html

marqLevAlg

Function optimization (minimization or maximization)

• Keywords: Optimization - Biostatistics

• Functional Description 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.

• Contact: Melanie Prague

• URL: https://cran.r-project.org/web/packages/marqLevAlg/index.html