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

Lihua J Zhu*, Claude Gazin, Nathan D Lawson, Hervé Pagès, Simon M Lin, David S Lapointe and Michael R Green

BMC Bioinformatics 2010, 11:237 doi:10.1186/1471-2105-11-237

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Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information

Hatice Osmanbeyoglu, Ryan J Hartmaier, Steffi Oesterreich, Xinghua Lu BMC Genomics 2012, 13(Suppl 1):S1 (17 January 2012)

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Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data

Iros Barozzi, Alberto Termanini, Saverio Minucci, Gioacchino Natoli Biology Direct 2011, 6:51 (6 October 2011)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Fish the ChIPs is a computational pipeline for complete ChIP-Seq data analysis of unlimited samples; it can be run on any Unix machine while providing a graphic interface for Mac.

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