chromstaR is a versatile computational algorithm for the analysis of single and/or multiple ChIP-seq experiments with or without replicates. The main motivation behind the algorithm is to be able to:
- infer combinatorial chromatin state maps based on ChIP-seq measurements of different histone modifications.
- detect changes in combinatorial chromatin state maps across different conditions such as experimental treatments, tissues, or developmental time points.
However, chromstaR can also be applied to more standard data analysis problems such as:
- analysis of ChIP-seq measurements of a single histone modification.
- comparison of ChIP-seq profiles of a single histone modification measured in different conditions, such as experimental treatments, tissues, or developmental time points.