DOI: 10.18129/B9.bioc.ChIPanalyser    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see ChIPanalyser.

ChIPanalyser: Predicting Transcription Factor Binding Sites

Bioconductor version: 3.12

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.

Author: Patrick C.N.Martin & Nicolae Radu Zabet

Maintainer: Patrick C.N. Martin <pm16057 at>

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


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biocViews Alignment, BiologicalQuestion, ChIPSeq, ChipOnChip, Coverage, DataImport, PeakDetection, SequenceMatching, Sequencing, Software, Transcription, WorkflowStep
Version 1.12.0
In Bioconductor since BioC 3.6 (R-3.4) (3.5 years)
License GPL-3
Depends R (>= 3.5.0), 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
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