Software

• adSplit - find annotation-driven splits
  A package exploring functional annotations to generate biologically motivated splits.
• compdiagTools - a toolbox for microarray analysis
  An R package containing tools for analysis and illustration of microarray experiments.
• DCOEX - finding groups of differentially coexpressed genes
  An algorithm for finding groups of genes which are differentially coexpressed between two phenotypically distinct types of samples.
• JALI - jumping alignments
  A new algorithm for amino acid sequence classification and the detection of remote homologs.
• MACAT - MicroArray Chromosome Analysis Tool
  An R/Bioconductor package for finding significantly differentially expressed chromosome regions.
• nem - Nested Effects Models
  An R/Bioconductor package to reconstruct phenotypic hierarchies from high-dimensional phenotying screens.
• OrderedList - Similarities of ordered gene lists
  An R/Bioconductor package to explore the similarity between two lists of ordered genes.
• StAM - Structured Analysis of Microarrays
  An R/Bioconductor package for decomposing complex phenotypes using biologically structured classification.
• TWILIGHT - Estimating the local false discovery rate
  An R/Bioconductor package for two-condition microarray experiments. Includes computation of scores, empirical p-values and local false discovery rates.

Packages we host for friends:

• isis - Identifying Splits with Clear Separation
  A class discovery method for gene expression data.
• oncomodel - Oncogenesis Modelling
  Computing probabilistic tree models for oncogenesis based on genetic data using maximum likelihood

All R-packages from our group are available from the CompDiag R repository.

In R, you can directly download a package by

library(reposTools)
pck = "stam" # or "twilight" or "macat" or ...
rep = getReposEntry("http://compdiag.molgen.mpg.de/software/Rrepos")
install.packages2(pck,rep)