RJMCMCNucleosomes

DOI: 10.18129/B9.bioc.RJMCMCNucleosomes  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Nucleosome Positioning
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, BiologicalQuestion, ChIPSeq, Coverage, NucleosomePositioning, Sequencing, Software, StatisticalMethod
Version	1.22.0
In Bioconductor since	BioC 3.5 (R-3.4) (6 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
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, rmarkdown, nucleoSim, RUnit
SystemRequirements	Rcpp
Enhances
URL	https://github.com/ArnaudDroitLab/RJMCMCNucleosomes
BugReports	https://github.com/ArnaudDroitLab/RJMCMCNucleosomes/issues
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	RJMCMCNucleosomes_1.22.0.tar.gz
Windows Binary	RJMCMCNucleosomes_1.22.0.zip
macOS Binary (x86_64)	RJMCMCNucleosomes_1.22.0.tgz
macOS Binary (arm64)	RJMCMCNucleosomes_1.22.0.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