This package implements functions for the combinatorial and differential analysis of ChIP-seq data. It was developed for histone modifications with a broad profile but is also suitable for the analysis of transcription factor binding data. A Hidden Markov Model with a mixture of Negative Binomials as emission densities is used to call peaks. Please refer to our manuscript at http://dx.doi.org/10.1101/038612 for a detailed description of the method.
The main function of this package is
Chromstar. For a detailed introduction type
browseVignettes("chromstaR") and read the vignette. Here is an overview of all
Aaron Taudt, Maria Colome-Tatche, Matthias Heinig, Minh Anh Nguyen