Package: ChIPanalyser
Type: Package
Title: ChIPanalyser: Predicting Transcription Factor Binding Sites
Authors@R: c(
    person(c("Patrick", "CN"), "Martin", role=c("cre", "aut"), email="pm16057@essex.ac.uk"),
    person(c("Nicolea","Radu"), "Zabet", role="aut"))
Version: 1.4.0
Date: 2017-09-01
Author: Patrick C.N.Martin & Nicolae Radu Zabet
Maintainer: Patrick C.N. Martin <pm16057@essex.ac.uk>
Citation: Zabet NR, Adryan B (2015) Estimating binding properties of
        transcription factors from genome-wide binding profiles.
        Nucleic Acids Res., 43, 84<e2><80><93>94.
Description: Based on a statistical thermodynamic framework, ChIPanalyser
    tries to produce ChIP-seq like profile.
    The model relies on four consideration:
    TF binding sites can be scored using a Position weight Matrix,
    DNA accessibility plays a role in Transcription Factor binding,
    binding profiles are dependant on	the number of transcription
    factors bound to DNA and finally binding energy
    (another way of describing PWM's) or binding specificity should be
    modulated (hence the introduction of a binding specificity modulator).
    The end result of ChIPanalyser is to produce profiles simulating
    real ChIP-seq profile and provide accuracy measurements
    of these predicted profiles after being compared to real ChIP-seq data.
    The ultimate goal is to produce ChIP-seq like profiles predicting ChIP-seq
    like profile to circumvent the need to produce costly ChIP-seq experiments.
License: GPL-3
Collate: 2AllS4Class_ProfileParameters.R 3AllGenerics.R 4AllMethods.R
        AllInitialize.R AllShowMethods.R computeChIPProfile.R
        computeOccupancy.R computeOptimal.R computePWMScore.R
        genomeWidePWM.R parallelInternalFunctions.R
        GenomicProfileGenericFunctions.R plotOccupancyDev.R
        plotOptimalHeatMapDev.R DataPreprocessing.R
        DataPreprocessingGenericFunctions.R profileAccuracyEstimate.R
Depends: R (>= 3.5.1),GenomicRanges, Biostrings, BSgenome, RcppRoll,
        parallel
Imports: methods, IRanges,
        S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR,
        BiocManager,GenomeInfoDb
Suggests: BSgenome.Dmelanogaster.UCSC.dm3,knitr, RUnit, BiocGenerics
Encoding: UTF-8
LazyData: true
biocViews: Software, BiologicalQuestion, WorkflowStep, Transcription,
        Sequencing, ChipOnChip, Coverage, Alignment, ChIPSeq,
        SequenceMatching, DataImport ,PeakDetection
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/ChIPanalyser
git_branch: RELEASE_3_8
git_last_commit: b5a2283
git_last_commit_date: 2018-10-30
Date/Publication: 2018-10-30
NeedsCompilation: no
Packaged: 2018-10-31 02:05:04 UTC; biocbuild
Built: R 3.5.1; ; 2018-12-17 11:27:01 UTC; unix
