RJMCMCNucleosomes

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

Bioconductor version: Release (3.20)

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 Deschênes [cre, aut], Khader Khadraoui [aut], Lajmi Lakhal-Chaieb [aut], Arnaud Droit [aut]

Maintainer: Astrid Deschênes <adeschen at hotmail.com>

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

Installation

To install this package, start R (version "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, BiologicalQuestion, ChIPSeq, Coverage, NucleosomePositioning, Sequencing, Software, StatisticalMethod
Version	1.30.0
In Bioconductor since	BioC 3.5 (R-3.4) (7.5 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

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_1.30.0.tar.gz
Windows Binary (x86_64)	RJMCMCNucleosomes_1.30.0.zip
macOS Binary (x86_64)	RJMCMCNucleosomes_1.30.0.tgz
macOS Binary (arm64)	RJMCMCNucleosomes_1.29.0.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