ChIPSeqSpike

DOI: 10.18129/B9.bioc.ChIPSeqSpike    

ChIP-Seq data scaling according to spike-in control

Bioconductor version: Release (3.8)

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>

Citation (from within R, enter citation("ChIPSeqSpike")):

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ChIPSeqSpike", version = "3.8")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ChIPSeqSpike")

 

PDF R Script ChIPSeqSpike
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, Coverage, DataImport, DifferentialMethylation, Epigenetics, HistoneModification, Normalization, Sequencing, Software, Transcription
Version 1.2.0
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
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package ChIPSeqSpike_1.2.0.tar.gz
Windows Binary ChIPSeqSpike_1.2.0.zip
Mac OS X 10.11 (El Capitan) ChIPSeqSpike_1.2.0.tgz
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 http://bioconductor.org/packages/ChIPSeqSpike/
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