patrickCNMartin/ChIPanalyserDev: ChIPanalyser: Predicting Transcription Factor Binding Sites

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.

Getting started

Package details

AuthorPatrick C.N.Martin & Nicolae Radu Zabet
Bioconductor views Alignment BiologicalQuestion ChIPSeq ChipOnChip Coverage DataImport PeakDetection SequenceMatching Sequencing Software Transcription WorkflowStep
MaintainerPatrick C.N. Martin <>
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
patrickCNMartin/ChIPanalyserDev documentation built on Nov. 14, 2019, 4:39 p.m.