Metadata-Version: 1.1
Name: MAnorm
Version: 1.1
Summary: A robust model for quantitative comparison of ChIP-Seq data sets.
Home-page: https://github.com/shao-lab/MAnorm
Author: Hayden Sun
Author-email: sunhongduo@picb.ac.cn
License: BSD
Description-Content-Type: UNKNOWN
Description: ChIP-Seq is widely used to characterize genome-wide binding patterns of transcription factors 
        and other chromatin-associated proteins. Although comparison of ChIP-Seq data sets is critical for understanding the 
        role of their cell type-specific binding on modulating gene regulation programs, few quantitative approaches have 
        been developed. Here, we present a simple and effective method, MAnorm, for quantitative comparison of ChIP-Seq data 
        sets describing transcription factor binding sites and epigenetic modifications. The quantitative binding differences 
        inferred by MAnorm showed strong correlation with both the changes in expression of target genes and the binding of 
        cell type-specific regulators. 
        
        MAnorm uses common peaks of two samples as a reference to build the rescaling model for normalization, which is based 
        on the empirical assumption that if a chromatin-associated protein has a substantial number of peaks shared in two 
        conditions, the binding at these common regions will tend to be determined by similar mechanisms, and thus should  
        exhibit similar global binding intensities across samples. 
        
        The normalized M value given by MAnorm was used as a quantitative measure of differential binding in each peak region 
        between two samples, with peak regions associated with larger absolute M values exhibiting greater binding differences 
        between two samples.  
        
        MAnorm exhibited excellent performance in quantitative comparison of ChIP-Seq data sets for both epigenetic 
        modifications and transcription factors. The quantitative binding differences inferred by MAnorm were highly 
        correlated with both the changes in expression of target genes and also the binding of cell type-specific regulators. 
        With the accumulation of ChIP-seq data sets, MAnorm should serve as a powerful tool for obtaining a more 
        comprehensive understanding of cell type-specific and cell state-specific regulation during organism development and 
        disease onset. 
        
        **Citation** MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ. Genome Biol. Mar 16;13(3):R16. 
        
        
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
