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ChIPanalyser

This is the development version of ChIPanalyser; for the stable release version, see ChIPanalyser.

ChIPanalyser: Predicting Transcription Factor Binding Sites


Bioconductor version: Development (3.19)

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 "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.25.0
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
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Suggests BSgenome.Dmelanogaster.UCSC.dm6, knitr, RUnit, BiocGenerics
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Package Archives

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

Source Package ChIPanalyser_1.25.0.tar.gz
Windows Binary ChIPanalyser_1.25.0.zip (64-bit only)
macOS Binary (x86_64) ChIPanalyser_1.25.0.tgz
macOS Binary (arm64)
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/
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