@article{Tu01012021,
author = {Tu, Shiqi and Li, Mushan and Chen, Haojie and Tan, Fengxiang and Xu, Jian and Waxman, David J. and Zhang, Yijing and Shao, Zhen}, 
title = {MAnorm2 for quantitatively comparing groups of ChIP-seq samples},
volume = {31}, 
number = {1}, 
pages = {131-145}, 
year = {2021}, 
doi = {10.1101/gr.262675.120}, 
abstract ={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.}, 
URL = {http://genome.cshlp.org/content/31/1/131.abstract}, 
eprint = {http://genome.cshlp.org/content/31/1/131.full.pdf+html}, 
journal = {Genome Research} 
}