ChIPanalyser

DOI: 10.18129/B9.bioc.ChIPanalyser    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see ChIPanalyser.

ChIPanalyser: Predicting Transcription Factor Binding Sites

Bioconductor version: 3.8

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 essex.ac.uk>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ChIPanalyser")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ChIPanalyser")

 

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

Details

biocViews	Alignment, BiologicalQuestion, ChIPSeq, ChipOnChip, Coverage, DataImport, PeakDetection, SequenceMatching, Sequencing, Software, Transcription, WorkflowStep
Version	1.4.0
In Bioconductor since	BioC 3.6 (R-3.4) (1.5 years)
License	GPL-3
Depends	R (>= 3.5.1), GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel
Imports	methods, IRanges, S4Vectors, grDevices, graphics, stats, utils, rtracklayer, ROCR, BiocManager, GenomeInfoDb
LinkingTo
Suggests	BSgenome.Dmelanogaster.UCSC.dm3, knitr, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ChIPanalyser_1.4.0.tar.gz
Windows Binary	ChIPanalyser_1.4.0.zip
Mac OS X 10.11 (El Capitan)	ChIPanalyser_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ChIPanalyser
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ChIPanalyser
Package Short Url	http://bioconductor.org/packages/ChIPanalyser/
Package Downloads Report	Download Stats