TY  - JOUR
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
Y1  - 2021/01/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 131 
EP  - 145 
DO  - 10.1101/gr.262675.120 
VL  - 31 
IS  - 1 
UR  - http://genome.cshlp.org/content/31/1/131.abstract 
N2  - 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. 
ER  -