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

Background: 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. Results: We have developed ChIPpeakAnno as a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched ge...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Lihua J. Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon M. Lin, David S. Lapointe, Michael R. Green
• Keywords: Binding Sites, BMCBI 2010, Large Number, Statistical Programming Environment