ChIPanalyser

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 gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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	R Script	ChIPanalyser User's Guide for Genetic Algorithms
PDF		Reference Manual
Text		NEWS

Details

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
LinkingTo
Suggests	BSgenome.Dmelanogaster.UCSC.dm6, 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_1.20.0.tar.gz
Windows Binary	ChIPanalyser_1.20.0.zip
macOS Binary (x86_64)	ChIPanalyser_1.20.0.tgz
macOS Binary (arm64)	ChIPanalyser_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ChIPanalyser
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ChIPanalyser
Bioc Package Browser	https://code.bioconductor.org/browse/ChIPanalyser/
Package Short Url	https://bioconductor.org/packages/ChIPanalyser/
Package Downloads Report	Download Stats