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R package for comparative analysis of RNA Polymerase II ChIP-Seq profiles by non-linear normalization
Marco A. Mendoza-Parra*, Martial Sankar*, Mannu Walia and Hinrich Gronemeyer
*These authors have contributed equally.
Nucleic Acid Research 2011; doi: 10.1093/nar/gkr1205

R package that integrates read-count signal intensity profiles with RNA Polymerase II binding site annotations to identify coding regions associated with potential transcriptional activity. Furthermore, POLYPHEMUS performs non-linear normalisation of multiple datasets prior to comparison, in order to correct for technical/experimental variations, which would otherwise complicate the interpretation of differences between compared samples and lead in extreme cases to false conclusions. As such POLYPHEMUS constitutes an integral part in an analytical pipeline devoted to the comparative analysis of multiple ChIP-seq data sets on PolII binding

 

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