CSREP

CSREP is a software tool that summarizes and compares chromatin state annotations across groups of biologically similar samples. It takes as input chromatin state maps for multiple samples and probabilistically estimates a representative chromatin state map for each group. CSREP uses an ensemble of multi-class logistic regression classifiers to predict the chromatin state assignment of each sample based on the state maps from all other samples. By comparing the probability assignments between two groups, CSREP can identify genomic locations with differential chromatin state assignments at a high resolution. The tool is useful for effectively summarizing information about chromatin state annotations within groups and identifying biologically relevant differences between groups.