ChIPComp specifications


Unique identifier OMICS_07536
Name ChIPComp
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Hao Wu

Publication for ChIPComp

ChIPComp citations


Recent advances in ChIP seq analysis: from quality management to whole genome annotation

Brief Bioinform
PMCID: 5444249
PMID: 26979602
DOI: 10.1093/bib/bbw023

[…] differential gene expression analysis [, ] can be used to directly compare more than two groups, and these methods do not consider the different S/Ns among samples either. In contrast, MAnorm [] and ChIPcomp [] are designed to consider different S/Ns. MAnorm scales the reads of peaks common to two samples using a robust linear regression based on the MA plot. ChIPcomp performs quantitative compar […]


A comprehensive comparison of tools for differential ChIP seq analysis

Brief Bioinform
PMCID: 5142015
PMID: 26764273
DOI: 10.1093/bib/bbv110

[…] enriched transcription factor binding sites.However, analysis of functional enrichments based on neighboring genes appears to be more robust.Some tools give good results with default parameters, like ChIPComp or diffBind when replicates are available, or MAnorm, Homer, macs2bdgdiff and RSEG with single replicates. The other tools would require more extensive fine-tuning of parameters to achieve sa […]

ChIPComp institution(s)
Department of Mathematics and Computer Science, Atlanta, GA, USA; Department of Biostatistics and Markey Cancer Center, University of Kentucky, Lexington, KY, USA; Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA; Department of Biomedical Informatics, Emory University, Atlanta, GA, USA
ChIPComp funding source(s)
Supported by the National Center for Advancing Translational Sciences of the National Institutes of Health under Award Number UL1TR000454, the National Human Genome Research Institute of the National Institutes of Health under Award Number R01 HG005119 and National Institute of General Medical Sciences of the National Institutes of Health under Award Number P01 GM085354.

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