PT - JOURNAL ARTICLE AU - Johannes Helmuth AU - Na Li AU - Laura Arrigoni AU - Kathrin Gianmoena AU - Cristina Cadenas AU - Gilles Gasparoni AU - Anupam Sinha AU - Philip Rosenstiel AU - Jörn Walter AU - Jan G. Hengstler AU - Thomas Manke AU - Ho-Ryun Chung TI - normR: Regime enrichment calling for ChIP-seq data AID - 10.1101/082263 DP - 2016 Jan 01 TA - bioRxiv PG - 082263 4099 - http://biorxiv.org/content/early/2016/10/20/082263.short 4100 - http://biorxiv.org/content/early/2016/10/20/082263.full AB - ChIP-seq probes genome-wide localization of DNA-associated proteins. To mitigate technical biases ChIP-seq read densities are normalized to read densities obtained by a control. Our statistical framework “normR” achieves a sensitive normalization by accounting for the effect of putative protein-bound regions on the overall read statistics. Here, we demonstrate normR’s suitability in three studies: (i) calling enrichment for high (H3K4me3) and low (H3K36me3) signal-to-ratio data; (ii) identifying two previously undescribed H3K27me3 and H3K9me3 heterochromatic regimes of broad and peak enrichment; and (iii) calling differential H3K4me3 or H3K27me3-enrichment between HepG2 hepatocarcinoma cells and primary human Hepatocytes. normR is readily available on http://bioconductor.org/packages/normrbpbase-pairCAGECap Analysis of Gene ExpressionChIP-seqChromatin Immunoprecipitation followed by next-generation sequencingEMExpectation MaximizationFDRFalse-Discovery RateGPIGlucose-6-Phosphate Isomerasekbkilo base-pairTSSTranscriptional Start SiteWGBSWhole Genome Bisulfite Sequencing