DESCRIPTION

Package: ChIPanalyser
Type: Package
Title: ChIPanalyser: Predicting Transcription Factor Binding Sites
Authors@R: c(
    person(c("Patrick", "CN"), "Martin", role=c("cre", "aut"), email="pcnmartin@gmail.com"),
    person(c("Nicolea","Radu"), "Zabet", role="aut"))
Version: 1.21.0
Date: 2017-09-01
Author: Patrick C.N.Martin & Nicolae Radu Zabet
Maintainer: Patrick C.N. Martin <pcnmartin@gmail.com>
Citation: Zabet NR, Adryan B (2015) Estimating binding properties of transcription
    factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
Description: ChIPanalyser is a package to predict and understand TF binding
    by utilizing a statistical thermodynamic model. The model incorporates 4
    main factors thought to drive TF binding: Chromatin State, Binding energy,
    Number of bound molecules and a scaling factor modulating TF binding
    affinity. Taken together, ChIPanalyser produces ChIP-like profiles that
    closely mimic the patterns seens in real ChIP-seq data. 
License: GPL-3
Collate: 2AllS4Class_ProfileParameters.R
	  3AllGenerics.R
	  4AllMethods.R
	  AllInitialize.R
	  AllShowMethods.R
	  computeChIPProfile.R
	  computeOccupancy.R
	  computeOptimal.R
	  computePWMScore.R
	  computeGenomeWide.R
	  parallelInternalFunctionsDev.R
	  GenomicProfileGenericFunctions.R
	  plotOccupancy.R
	  plotOptimalHeatMapDev.R
	  DataPreprocessingDev.R
	  DataPreprocessingGenericFunctionsDev.R
	  profileAccuracyEstimateDev.R
	  GAAnalysis.R
    GAGeneric.R
Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel
Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb,RColorBrewer
Suggests: BSgenome.Dmelanogaster.UCSC.dm6,knitr, RUnit, BiocGenerics
Encoding: UTF-8
LazyData: true
biocViews: Software, BiologicalQuestion, WorkflowStep, Transcription,
    Sequencing, ChipOnChip, Coverage, Alignment, ChIPSeq, SequenceMatching,
    DataImport ,PeakDetection
VignetteBuilder: knitr
RoxygenNote: 7.2.1