ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.

Publication Type:

Journal Article

Source:

BMC bioinformatics, Volume 11, p.237 (2010)

Keywords:

Binding Sites, Chromatin Immunoprecipitation, GENOME, Oligonucleotide Array Sequence Analysis, Public Health Sciences Division, Software

Abstract:

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome.