ChIPSeqSpike

DOI: 10.18129/B9.bioc.ChIPSeqSpike    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ChIPSeqSpike.

ChIP-Seq data scaling according to spike-in control

Bioconductor version: 3.13

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 gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ChIPSeqSpike")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	ChIPSeq, Coverage, DataImport, DifferentialMethylation, Epigenetics, HistoneModification, ImmunoOncology, Normalization, Sequencing, Software, Transcription
Version	1.12.0
In Bioconductor since	BioC 3.7 (R-3.5) (3.5 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
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Suggests	BiocStyle, knitr, rmarkdown, testthat
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary	ChIPSeqSpike_1.12.0.zip
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/ChIPSeqSpike
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ChIPSeqSpike
Package Short Url	https://bioconductor.org/packages/ChIPSeqSpike/
Package Downloads Report	Download Stats