RJMCMCNucleosomes
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RJMCMCNucleosomes.
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
Bioconductor version: 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 Deschênes [cre, aut], Khader Khadraoui [aut], Lajmi Lakhal-Chaieb [aut], Arnaud Droit [aut]
Maintainer: Astrid Deschênes <adeschen at hotmail.com>
citation("RJMCMCNucleosomes")):
Installation
To install this package, start R (version "3.6") 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")| Nucleosome Positioning | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, BiologicalQuestion, ChIPSeq, Coverage, NucleosomePositioning, Sequencing, Software, StatisticalMethod |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 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 |
| System Requirements | Rcpp |
| URL | https://github.com/ArnaudDroitLab/RJMCMCNucleosomes |
| Bug Reports | https://github.com/ArnaudDroitLab/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_1.8.0.tar.gz |
| Windows Binary | RJMCMCNucleosomes_1.8.0.zip |
| Mac OS X 10.11 (El Capitan) | RJMCMCNucleosomes_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RJMCMCNucleosomes |
| Source Repository (Developer Access) | git clone [email protected]:packages/RJMCMCNucleosomes |
| Bioc Package Browser | https://code.bioconductor.org/browse/RJMCMCNucleosomes/ |
| Package Short Url | https://bioconductor.org/packages/RJMCMCNucleosomes/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |