DOI: 10.18129/B9.bioc.ChIPanalyser  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ChIPanalyser.

ChIPanalyser: Predicting Transcription Factor Binding Sites

Bioconductor version: 3.16

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.

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

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

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


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PDF R Script ChIPanalyser User's Guide
PDF R Script ChIPanalyser User's Guide for Genetic Algorithms
PDF   Reference Manual
Text   NEWS


biocViews Alignment, BiologicalQuestion, ChIPSeq, ChipOnChip, Coverage, DataImport, PeakDetection, SequenceMatching, Sequencing, Software, Transcription, WorkflowStep
Version 1.20.0
In Bioconductor since BioC 3.6 (R-3.4) (5.5 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, RColorBrewer
Suggests BSgenome.Dmelanogaster.UCSC.dm6, knitr, RUnit, BiocGenerics
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