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. 2012 Jan 1;28(1):121-2.
doi: 10.1093/bioinformatics/btr605. Epub 2011 Nov 3.

Detecting differential binding of transcription factors with ChIP-seq

Kun Liang  1 , Sündüz Keles
Affiliations

Detecting differential binding of transcription factors with ChIP-seq

Kun Liang et al. Bioinformatics. .

Abstract

Summary: Increasing number of ChIP-seq experiments are investigating transcription factor binding under multiple experimental conditions, for example, various treatment conditions, several distinct time points and different treatment dosage levels. Hence, identifying differential binding sites across multiple conditions is of practical importance in biological and medical research. To this end, we have developed a powerful and flexible program, called DBChIP, to detect differentially bound sharp binding sites across multiple conditions, with or without matching control samples. By assigning uncertainty measure to the putative differential binding sites, DBChIP facilitates downstream analysis. DBChIP is implemented in R programming language and can work with a wide range of sequencing file formats.

Availability: R package DBChIP is available at http://pages.cs.wisc.edu/~kliang/DBChIP/ CONTACT: kliang@stat.wisc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Workflow of DBChIP.
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