@article {Helmuth082263, author = {Johannes Helmuth and Na Li and Laura Arrigoni and Kathrin Gianmoena and Cristina Cadenas and Gilles Gasparoni and Anupam Sinha and Philip Rosenstiel and J{\"o}rn Walter and Jan G. Hengstler and Thomas Manke and Ho-Ryun Chung}, title = {normR: Regime enrichment calling for ChIP-seq data}, elocation-id = {082263}, year = {2016}, doi = {10.1101/082263}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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 {\textquotedblleft}normR{\textquotedblright} achieves a sensitive normalization by accounting for the effect of putative protein-bound regions on the overall read statistics. Here, we demonstrate normR{\textquoteright}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/normr}, URL = {https://www.biorxiv.org/content/early/2016/10/25/082263}, eprint = {https://www.biorxiv.org/content/early/2016/10/25/082263.full.pdf}, journal = {bioRxiv} }