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 (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RJMCMCNucleosomes")

Documentation

HTML	R Script	Nucleosome Positioning
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, BiologicalQuestion, ChIPSeq, Coverage, NucleosomePositioning, Sequencing, Software, StatisticalMethod
Version	1.2.0
In Bioconductor since	BioC 3.5 (R-3.4) (1 year)
License	Artistic-2.0
Depends	R (>= 3.4), IRanges, GenomicRanges
Imports	Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb, S4Vectors, 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
Build Report

Package Archives

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

Source Package	RJMCMCNucleosomes_1.2.0.tar.gz
Windows Binary	RJMCMCNucleosomes_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	RJMCMCNucleosomes_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RJMCMCNucleosomes
Package Short Url	http://bioconductor.org/packages/RJMCMCNucleosomes/
Package Downloads Report	Download Stats