ChIPanalyser

DOI: 10.18129/B9.bioc.ChIPanalyser    

ChIPanalyser: Predicting Transcription Factor Binding Sites

Bioconductor version: Release (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")

 

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 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
Package Short Url https://bioconductor.org/packages/ChIPanalyser/
Package Downloads Report Download Stats

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