ChIPSeqSpike

This package is for version 3.9 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: 3.9

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 (version "3.6") and enter:


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

BiocManager::install("ChIPSeqSpike")

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

Documentation

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

browseVignettes("ChIPSeqSpike")
ChIPSeqSpike PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, Coverage, DataImport, DifferentialMethylation, Epigenetics, HistoneModification, ImmunoOncology, Normalization, Sequencing, Software, Transcription
Version 1.4.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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 ChIPSeqSpike_1.4.0.tar.gz
Windows Binary ChIPSeqSpike_1.4.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) ChIPSeqSpike_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ChIPSeqSpike
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ChIPSeqSpike
Bioc Package Browser https://code.bioconductor.org/browse/ChIPSeqSpike/
Package Short Url https://bioconductor.org/packages/ChIPSeqSpike/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive