RJMCMCNucleosomes
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
Bioconductor version: Release (3.19)
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("RJMCMCNucleosomes")
):
Installation
To install this package, start R (version "4.4") 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 | 1.28.0 |
In Bioconductor since | BioC 3.5 (R-3.4) (7.5 years) |
License | Artistic-2.0 |
Depends | R (>= 3.5.0), IRanges, GenomicRanges |
Imports | Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb, S4Vectors(>= 0.23.10), 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_1.28.0.tar.gz |
Windows Binary | RJMCMCNucleosomes_1.28.0.zip |
macOS Binary (x86_64) | RJMCMCNucleosomes_1.28.0.tgz |
macOS Binary (arm64) | RJMCMCNucleosomes_1.28.0.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 |