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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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_1.37.0.zip |
| macOS Binary (big-sur-x86_64) | RJMCMCNucleosomes_1.37.0.tgz |
| macOS Binary (sonoma-arm64) | RJMCMCNucleosomes_1.37.0.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 |