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).
A software package for (integrative and meta-analytic) network modeling and analysis.
ShrinkBayes: Bayesian differential expression analysis for RNAseq, microarray or RNAi-screens data.
A software package for the joint analysis of high-throughput data from multiple molecular levels.
GRridge: Better prediction by use of co-data: adaptive group-regularized regression.
globalSeq: global test for counts; testing for association between RNA-Seq and high-dimensional data.
semisup: semi-supervised mixture model; detecting SNPs with interactive effect on a quantitative trait.
The package reconstructs and exploits networks from time course data.
R-package to estimate group-regularized logistic elastic net regression models for high-dimensional data, with the inclusion of external information.
palasso: paired lasso; sparse regression with paired covariates.