chromstaR-package: Combinatorial and differential chromatin state analysis for ChIP-seq data


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 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 plotting functions.


Aaron Taudt, Maria Colome-Tatche, Matthias Heinig, Minh Anh Nguyen

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