Package: RJMCMCNucleosomes
Version: 1.37.1
Date: 2025-07-28
Title: Bayesian hierarchical model for genome-wide nucleosome
        positioning with high-throughput short-read data (MNase-Seq)
Description: 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).
Authors@R: c(person("Pascal", "Belleau",
    email="pascal_belleau@hotmail.com", role=c("aut"), 
    comment=c(ORCID="0000-0002-0802-1071")),
    person("Rawane", "Samb",
    email="rawane.samb.1@ulaval.ca", role=c("aut")),
    person("Astrid", "Deschênes",
    email="adeschen@hotmail.com",
    role=c("cre","aut"), comment=c(ORCID="0000-0001-7846-6749")),
    person("Khader", "Khadraoui",
    email="Khader.Khadraoui@mat.ulaval.ca", role=c("aut")),
    person("Lajmi", "Lakhal-Chaieb",
    email="Lajmi.Lakhal@mat.ulaval.ca;", role=c("aut")),
    person("Arnaud", "Droit",
    email="arnaud.droit@crchuq.ulaval.ca", role=c("aut")))
Depends: R (>= 4.5.0), IRanges, GenomicRanges
Imports: Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, Seqinfo,
        S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods,
        grDevices
Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit
LinkingTo: Rcpp
SystemRequirements: Rcpp
Encoding: UTF-8
License: Artistic-2.0
URL: https://github.com/adeschen/RJMCMCNucleosomes
BugReports: https://github.com/adeschen/RJMCMCNucleosomes/issues
VignetteBuilder: knitr
biocViews: BiologicalQuestion, ChIPSeq, NucleosomePositioning,
        Software, StatisticalMethod, Bayesian, Sequencing, Coverage
Config/roxygen2/version: 8.1.0
git_url: https://git.bioconductor.org/packages/RJMCMCNucleosomes
git_branch: devel
git_last_commit: 519915a
git_last_commit_date: 2026-11-03
Repository: Bioconductor 3.24
Date/Publication: 2026-11-04
NeedsCompilation: yes
Packaged: 2026-11-05 01:03:32 UTC; biocbuild
Author: Pascal Belleau [aut] (ORCID: <https://orcid.org/0000-0002-0802-1071>),
  Rawane Samb [aut],
  Astrid Deschênes [cre, aut] (ORCID:
    <https://orcid.org/0000-0001-7846-6749>),
  Khader Khadraoui [aut],
  Lajmi Lakhal-Chaieb [aut],
  Arnaud Droit [aut]
Maintainer: Astrid Deschênes <adeschen@hotmail.com>
