Our software

Our group develops software, either as part of research projects where new methods are developed, or as newer and efficient implementations of existing methods. Mostly we implement methods as R packages, which as R are open source and free. Packages can be downloaded and installed in any computer where R is installed.

Here we give a summary of available software developed by our group, with links to where software packages themselves can be found. Links to additional packages, including those developed by former group members, are available from the personal web sites of Wessel van Wieringen (link) and Mark van de Wiel (link).

 

Software packages

rags2ridges

A software package for (integrative and meta-analytic) network modeling and analysis.

ShrinkBayes

ShrinkBayes: Bayesian differential expression analysis for RNAseq, microarray or RNAi-screens data.

sigaR

A software package for the joint analysis of high-throughput data from multiple molecular levels.

GRridge

GRridge: Better prediction by use of co-data: adaptive group-regularized regression.

DNACopyNumber

Several packages for analysing DNA copy number data, in collaboration with the Tumor Genome Analysis Core.

globalSeq

Use this package to test for association between RNA-Seq and high-dimensional data.

semisup

Use this package to test whether a SNP has an interactive effect on a quantitative trait.

ragt2ridges

The package reconstructs and exploits networks from time course data.