normR: Regime enrichment calling for ChIP-seq data

Helmuth, J.; Li, N.; Arrigoni, L.; Gianmoena, K.; Cadenas, C.; Gasparoni, G.; Sinha, A.; Rosenstiel, P.; Walter, J.; Hengstler, J. G.; Manke, T.; Chung, H.-R.

doi:10.1101/082263

bioRxiv · 10.1101/082263

normR: Regime enrichment calling for ChIP-seq data

Helmuth, J.·Li, N.·Arrigoni, L.·Gianmoena, K.·Cadenas, C.·Gasparoni, G.·Sinha, A.·Rosenstiel, P.·Walter, J.·Hengstler, J. G.·Manke, T.·Chung, H.-R.

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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 \"normR\" achieves a sensitive normalization by accounting for the effect of putative protein-bound regions on the overall read statistics. Here, we demonstrate normRs 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

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Helmuth, J., Li, N., Arrigoni, L., Gianmoena, K., Cadenas, C., Gasparoni, G., Sinha, A., Rosenstiel, P., Walter, J., Hengstler, J. G., Manke, T., Chung, H.-R.. 2016-10-20. normR: Regime enrichment calling for ChIP-seq data. https://doi.org/10.1101/082263

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