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RJMCMCNucleosomes

Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)


Bioconductor version: Release (3.18)

This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.

Author: Pascal Belleau [aut], Rawane Samb [aut], Astrid DeschĂȘnes [cre, aut], Khader Khadraoui [aut], Lajmi Lakhal-Chaieb [aut], Arnaud Droit [aut]

Maintainer: Astrid DeschĂȘnes <adeschen at hotmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("RJMCMCNucleosomes")

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("RJMCMCNucleosomes")
Nucleosome Positioning HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, BiologicalQuestion, ChIPSeq, Coverage, NucleosomePositioning, Sequencing, Software, StatisticalMethod
Version 1.26.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License Artistic-2.0
Depends R (>= 3.5.0), IRanges, GenomicRanges
Imports Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb, S4Vectors(>= 0.23.10), BiocParallel, stats, graphics, methods, grDevices
System Requirements Rcpp
URL https://github.com/ArnaudDroitLab/RJMCMCNucleosomes
Bug Reports https://github.com/ArnaudDroitLab/RJMCMCNucleosomes/issues
See More
Suggests BiocStyle, knitr, rmarkdown, nucleoSim, RUnit
Linking To Rcpp
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 RJMCMCNucleosomes_1.26.0.tar.gz
Windows Binary RJMCMCNucleosomes_1.26.0.zip
macOS Binary (x86_64) RJMCMCNucleosomes_1.26.0.tgz
macOS Binary (arm64) RJMCMCNucleosomes_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RJMCMCNucleosomes
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RJMCMCNucleosomes
Bioc Package Browser https://code.bioconductor.org/browse/RJMCMCNucleosomes/
Package Short Url https://bioconductor.org/packages/RJMCMCNucleosomes/
Package Downloads Report Download Stats