ChIPpeakAnno (2010)

» A bioconductor package for batch annotating peaks identified from ChIP-seq, ChIP-chip or any experiments that result in large number of genomic interval data

Description:
Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages.

Publications:
Zhu L (2013). "Integrative analysis of ChIP-chip and ChIP-seq dataset.” In Lee T, Luk ACS (eds.), Tilling Arrays, volume 1067, chapter 4, -19. Humana Press.  

Zhu LJ*, Gazin C, Lawson ND, Pages H, Lin SM, Lapointe DS and Green MR. (2010) [* denotes corresponding author] ChIPpeakAnno: A Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics. 2010, 11:237.