Package: ChIPSeqSpike
Type: Package
Title: ChIP-Seq data scaling according to spike-in control
Version: 1.9.0
Date: 2018-04-11
Author: Nicolas Descostes
Maintainer: Nicolas Descostes <nicolas.descostes@gmail.com>
Description: 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.
License: Artistic-2.0
Imports: tools, stringr, Rsamtools, GenomicRanges, IRanges, seqplots,
        ggplot2, LSD, corrplot, methods, stats, grDevices, graphics,
        utils, BiocGenerics, S4Vectors
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown, testthat
Depends: R (>= 3.5), rtracklayer (>= 1.37.6)
biocViews: ImmunoOncology, ChIPSeq, Sequencing, Normalization,
        Transcription, Coverage, DifferentialMethylation, Epigenetics,
        DataImport, HistoneModification
git_url: https://git.bioconductor.org/packages/ChIPSeqSpike
git_branch: master
git_last_commit: 401147a
git_last_commit_date: 2020-04-27
Date/Publication: 2020-04-27
NeedsCompilation: no
Packaged: 2020-04-28 02:46:58 UTC; biocbuild
Built: R 4.0.3; ; 2021-03-30 23:43:55 UTC; unix
