RJMCMCNucleosomes

DOI: 10.18129/B9.bioc.RJMCMCNucleosomes    

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

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

Bioconductor version: Development (3.9)

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 "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("RJMCMCNucleosomes", version = "3.9")

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 1.7.0
In Bioconductor since BioC 3.5 (R-3.4) (1.5 years)
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
Links To Me
Build Report  

Package Archives

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

Source Package RJMCMCNucleosomes_1.7.0.tar.gz
Windows Binary RJMCMCNucleosomes_1.7.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) RJMCMCNucleosomes_1.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RJMCMCNucleosomes
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RJMCMCNucleosomes
Package Short Url http://bioconductor.org/packages/RJMCMCNucleosomes/
Package Downloads Report Download Stats

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