Software:
On this page you find open-source programs developed in our group that implement various of our methods and algorithms.
R Packages:
All of our R packages have been deposited on CRAN, so that you
can install them easily from within R.
- corpcor: Efficient estimation of covariance and (partial) correlation.
- entropy: Entropy and mutual information estimation.
- fdrtool: Estimation and control of (local) false discovery rates.
- GeneNet: Modeling and inferring gene networks.
- longitudinal: Analysis of multiple time course data.
- sda: Shrinkage discriminant analysis and feature selection.
- st: Shrinkage t statistic and correlation-adjusted t score.
- ape:
Analyses of phylogenetics and evolution
(Maintainer: E. Paradis) - GeneCycle:
Identification of periodically expressed genes
(Maintainer: M. Ahdesmäki). - plsgenomics:
PLS analyses for genomics
(Maintainer: A. Boulesteix).
Other R Code:
- R code for shrinkage estimation of VAR network.
Matlab/Octave Code:
This code was kindly contributed by Kevin P. Murphy.
- Shrinkage covariance and correlation estimation
(README):
covshrink-kpm.zip (all files together in a ZIP archive),
covshrinkKPM.m (Matlab function),
testscript-matlab.txt, testscript-R.txt (test scripts),
smalldata.txt, largedata.txt (example data files).
Miscellaneous:
- TREE-PUZZLE: Maximum-likelihood tree reconstruction package.
- PAL: Java library for methods in molecular sequence analysis.
- Vanilla: Java command line programs based on PAL.
Last modified:
December 13, 2008
December 13, 2008