ChIPComp is an R package for quantatitive comparison of multiple ChIP-seq datasets. ChIPComp improves the differential protein binding or histone modification analyses for ChIP-seq data by properly considering the background information from control samples and different signal to noise ratios. ChIPComp also works for general experimental design.
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A novel statistical method for quantitative comparison of multiple ChIP-seq datasets.
Chen L, Wang C, Qin ZS, Wu H.
Bioinformatics. 2015 Feb 13. pii: btv094.