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 (3.24)
This package detects nucleosome positions genome-wide from paired-end or single-end MNase-Seq reads using a Bayesian hierarchical model. Read positions are modelled as a mixture of Student's t-distributions with an informative Multinomial-Dirichlet prior on nucleosome locations, and the number of nucleosomes is estimated with a reversible jump Markov chain Monte Carlo (RJMCMC) algorithm. Functions are provided to split chromosomes into segments for parallel analysis, merge and post-process the predictions, and plot nucleosome positions alongside read coverage. This package implements the method described in Samb et al. 2015 (DOI:10.1515/sagmb-2014-0098).
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("RJMCMCNucleosomes")):Pascal Belleau, Rawane Samb, Astrid Deschênes, Khader Khadraoui, Lajmi Lakhal-Chaieb, Arnaud Droit. RJMCMCNucleosomes: Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq). doi:10.18129/B9.bioc.RJMCMCNucleosomes, R package version 1.37.1, https://bioconductor.org/packages/RJMCMCNucleosomes.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | ||
| NEWS | Text |
Details
| biocViews | Bayesian, BiologicalQuestion, ChIPSeq, Coverage, NucleosomePositioning, Sequencing, Software, StatisticalMethod |
| Version | 1.37.1 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0), IRanges, GenomicRanges |
| Imports | Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, Seqinfo, S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods, grDevices |
| System Requirements | Rcpp |
| URL | https://github.com/adeschen/RJMCMCNucleosomes |
| Bug Reports | https://github.com/adeschen/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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RJMCMCNucleosomes_1.37.1.tar.gz |
| Windows Binary (x86_64) | RJMCMCNucleosomes_1.37.1.zip |
| macOS Binary (big-sur-x86_64) | RJMCMCNucleosomes_1.37.1.tgz |
| macOS Binary (sonoma-arm64) | RJMCMCNucleosomes_1.37.1.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 | https://bioconductor.org/packages/RJMCMCNucleosomes/ |
| Package Downloads Report | Download Stats |