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>

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

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

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) (6.5 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
System Requirements
URL
See More
Suggests BSgenome.Dmelanogaster.UCSC.dm6, knitr, RUnit, BiocGenerics
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report 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
Old Source Packages for BioC 3.16 Source Archive