RT Journal
A1 Tu, Shiqi
A1 Li, Mushan
A1 Chen, Haojie
A1 Tan, Fengxiang
A1 Xu, Jian
A1 Waxman, David J.
A1 Zhang, Yijing
A1 Shao, Zhen
T1 MAnorm2 for quantitatively comparing groups of ChIP-seq samples
JF Genome Research 
JO Genome Research 
YR 2021 
FD January 01 
VO 31 
IS 1 
SP 131 
OP 145 
DO 10.1101/gr.262675.120 
UL http://genome.cshlp.org/content/31/1/131.abstract 
AB Eukaryotic gene transcription is regulated by a large cohort of chromatin-associated proteins, and inferring their differential binding sites between cellular contexts requires a rigorous comparison of the corresponding ChIP-seq data. We present MAnorm2, a new computational tool for quantitatively comparing groups of ChIP-seq samples. MAnorm2 uses a hierarchical strategy for normalization of ChIP-seq data and assesses within-group variability of ChIP-seq signals based on an empirical Bayes framework. In this framework, MAnorm2 allows for abundant differential ChIP-seq signals between groups of samples as well as very different global within-group variability between groups. Using a number of real ChIP-seq data sets, we observed that MAnorm2 clearly outperformed existing tools for differential ChIP-seq analysis, especially when the groups of samples being compared had distinct global within-group variability.