Statistics and Computational Biology
On this page you find computer programs developed in our group. They are all free software (GNU GPL) and provide reference implementation for our methods.
All of our R packages have been deposited on CRAN, so that you
can install them easily from within R.
R packages - computational biology:
- GeneCycle: Identification of periodically expressed genes.
- GeneNet: Modeling and inferring gene networks.
- MALDIquant: Quantitative analysis of mass spectrometry data.
- MALDIquantForeign: Import/export routines for MALDIquant.
- readBrukerFlexData: Read MS data in Bruker *flex format.
- readMzXmlData: Read MS data in mzXML format.
- Contributions to ape (phylogenetics in R) and plsgenomics.
- R code for shrinkage estimation of VAR gene network.
R packages - statistical methods:
- care: High-dimensional regression and CAR score variable selection.
- corpcor: Efficient estimation of covariance and (partial) correlation.
- entropy: Entropy and mutual information estimation.
- fdrtool: Estimation of (local) false discovery rates and higher criticism.
- longitudinal: Analysis of multiple time course data.
- sda: Shrinkage discriminant analysis and CAT score variable selection.
- st: Shrinkage t statistic and CAT score.
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).
Phylogenetics:
- 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:
February 16, 2011
February 16, 2011