DOI: 10.18129/B9.bioc.ChIPanalyser    

This is the development version of ChIPanalyser; for the stable release version, see ChIPanalyser.

ChIPanalyser: Predicting Transcription Factor Binding Sites

Bioconductor version: Development (3.7)

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 CN Martin [cre, aut], Nicolea Radu Zabet [aut]

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

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biocViews Alignment, BiologicalQuestion, ChIPSeq, ChipOnChip, Coverage, DataImport, PeakDetection, SequenceMatching, Sequencing, Software, Transcription, WorkflowStep
Version 1.1.1
License GPL-3
Depends R (>= 3.4.1), GenomicRanges, Biostrings, BSgenome, RcppRoll
Imports methods, IRanges, S4Vectors, grDevices, graphics, stats, utils
Suggests BSgenome.Dmelanogaster.UCSC.dm3, knitr, RUnit, BiocGenerics
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