DOI: 10.18129/B9.bioc.ChIPSeqSpike    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see ChIPSeqSpike.

ChIP-Seq data scaling according to spike-in control

Bioconductor version: 3.12

Chromatin Immuno-Precipitation followed by Sequencing (ChIP-Seq) is used to determine the binding sites of any protein of interest, such as transcription factors or histones with or without a specific modification, at a genome scale. The many steps of the protocol can introduce biases that make ChIP-Seq more qualitative than quantitative. For instance, it was shown that global histone modification differences are not caught by traditional downstream data normalization techniques. A case study reported no differences in histone H3 lysine-27 trimethyl (H3K27me3) upon Ezh2 inhibitor treatment. To tackle this problem, external spike-in control were used to keep track of technical biases between conditions. Exogenous DNA from a different non-closely related species was inserted during the protocol to infer scaling factors that enabled an accurate normalization, thus revealing the inhibitor effect. ChIPSeqSpike offers tools for ChIP-Seq spike-in normalization. Ready to use scaled bigwig files and scaling factors values are obtained as output. ChIPSeqSpike also provides tools for ChIP-Seq spike-in assessment and analysis through a versatile collection of graphical functions.

Author: Nicolas Descostes

Maintainer: Nicolas Descostes <nicolas.descostes at>

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biocViews ChIPSeq, Coverage, DataImport, DifferentialMethylation, Epigenetics, HistoneModification, ImmunoOncology, Normalization, Sequencing, Software, Transcription
Version 1.9.0
In Bioconductor since BioC 3.7 (R-3.5) (3 years)
License Artistic-2.0
Depends R (>= 3.5), rtracklayer(>= 1.37.6)
Imports tools, stringr, Rsamtools, GenomicRanges, IRanges, seqplots, ggplot2, LSD, corrplot, methods, stats, grDevices, graphics, utils, BiocGenerics, S4Vectors
Suggests BiocStyle, knitr, rmarkdown, testthat
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