Package: RJMCMCNucleosomes 1.35.0

Astrid Deschênes

RJMCMCNucleosomes: Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

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.

Authors:Pascal Belleau [aut], Rawane Samb [aut], Astrid Deschênes [cre, aut], Khader Khadraoui [aut], Lajmi Lakhal-Chaieb [aut], Arnaud Droit [aut]

RJMCMCNucleosomes_1.35.0.tar.gz
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RJMCMCNucleosomes.pdf |RJMCMCNucleosomes.html✨
RJMCMCNucleosomes/json (API)
NEWS

# Install 'RJMCMCNucleosomes' in R:
install.packages('RJMCMCNucleosomes', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/arnauddroitlab/rjmcmcnucleosomes/issues

Uses libs:
  • gsl– GNU Scientific Library (GSL)
  • c++– GNU Standard C++ Library v3
Datasets:
  • reads_demo_01 - Forward reads and reverse reads in 'GRanges' format (for demo purpose).
  • reads_demo_02 - Forward reads and reverse reads in 'GRanges' format (for demo purpose).
  • RJMCMC_result - Nucleosomes obtained by running RJMCMC function using reads from reads_demo_02 dataset (for demo purpose).
  • syntheticNucleosomeReads - Simulated dataset of reads generated by 'nucleoSim' package (for demo purpose).

On BioConductor:RJMCMCNucleosomes-1.35.0(bioc 3.23)RJMCMCNucleosomes-1.34.0(bioc 3.22)

biologicalquestionchipseqnucleosomepositioningsoftwarestatisticalmethodbayesiansequencingcoveragebayesian-t-mixturebioconductorc-plus-plusgenome-wide-profilingmultinomial-dirichlet-priornucleosome-positioningnucleosomesreversible-jump-mcmcgslcpp

4.60 score 1 scripts 344 downloads 7 exports 58 dependencies

Last updated from:e3d8d0ff4c. Checks:1 WARNING, 11 NOTE, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING189
linux-devel-arm64NOTE305
linux-devel-x86_64NOTE377
source / vignettesOK293
linux-release-arm64NOTE296
linux-release-x86_64NOTE356
macos-release-arm64NOTE256
macos-release-x86_64NOTE662
macos-oldrel-arm64NOTE203
macos-oldrel-x86_64NOTE488
windows-develNOTE352
windows-releaseNOTE337
windows-oldrelNOTE348
wasm-releaseFAIL147

Exports:mergeAllRDSFilesFromDirectorymergeRDSFilesplotNucleosomespostTreatmentrjmcmcrjmcmcCHRsegmentation

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodetoolsconsensusSeekeRcpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslR6RcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystringistringrSummarizedExperimentsysvctrsXMLXVectoryaml

Nucleosome Positioning

Rendered fromRJMCMCNucleosomes.Rmdusingknitr::rmarkdownon Apr 12 2026.

Last update: 2016-12-19
Started: 2016-12-19

Readme and manuals

Help Manual

Help pageTopics
RJMCMCNucleosomes: Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)RJMCMCNucleosomes-package RJMCMCNucleosomes
Merge nucleosome information from all RDS files present in a same directory. Beware that only nucleosome information from same chromosome should be merged together.mergeAllRDSFilesFromDirectory
Merge nucleosome information from selected RDS files.mergeRDSFiles
Generate a graph of nucleosome positions with read coverageplotNucleosomes
A post-treatment function to merge closely positioned nucleosomes, from the same chromosome, identified by the 'rjmcmc' function.postTreatment
Formated output of predicted nucleosomesprint.rjmcmcNucleosomes
Formated output of predicted nucleosomesprint.rjmcmcNucleosomesBeforeAndAfterPostTreatment
Formated output of predicted nucleosomesprint.rjmcmcNucleosomesMerge
Forward reads and reverse reads in 'GRanges' format (for demo purpose).reads_demo_01
Forward reads and reverse reads in 'GRanges' format (for demo purpose).reads_demo_02
Nucleosome positioning mapping on a segmentrjmcmc
Nucleosomes obtained by running RJMCMC function using reads from reads_demo_02 dataset (for demo purpose).RJMCMC_result
Nucleosome positioning mapping on a large segment, up to a chromosomerjmcmcCHR
Split a 'GRanges' containing reads in a list of smaller segments for the 'rjmcmc' function.segmentation
Simulated dataset of reads generated by 'nucleoSim' package (for demo purpose).syntheticNucleosomeReads