Package: RJMCMCNucleosomes 1.36.0

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]

# Install 'RJMCMCNucleosomes' in R:

install.packages('RJMCMCNucleosomes', repos = c('https://bioc-release.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-1.37.0(bioc 3.24)RJMCMCNucleosomes-1.36.0(bioc 3.23)

biologicalquestion chipseq nucleosomepositioning software statisticalmethod bayesian sequencing coverage bayesian-t-mixture bioconductor c-plus-plus genome-wide-profiling multinomial-dirichlet-prior nucleosome-positioning nucleosomes reversible-jump-mcmc gsl cpp

4.30 score 3 scripts 602 downloads 7 exports 58 dependencies

Last updated from:fea8323b7b (on RELEASE_3_23). Checks:1 WARNING, 13 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	223
linux-devel-arm64	NOTE	321
linux-devel-x86_64	NOTE	376
source / vignettes	OK	264
linux-release-arm64	NOTE	305
linux-release-x86_64	NOTE	388
macos-release-arm64	NOTE	315
macos-release-x86_64	NOTE	398
macos-oldrel-arm64	NOTE	227
macos-oldrel-x86_64	NOTE	567
windows-devel-arm64	NOTE	384
windows-devel-x86_64	NOTE	356
windows-release-arm64	NOTE	365
windows-release-x86_64	NOTE	341
windows-oldrel-x86_64	NOTE	334
wasm-release	OK	163

Exports:mergeAllRDSFilesFromDirectory mergeRDSFiles plotNucleosomes postTreatment rjmcmc rjmcmcCHR segmentation

Dependencies:abind askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops cigarillo cli codetools consensusSeekeR cpp11 crayon curl DelayedArray formatR futile.logger futile.options generics GenomicAlignments GenomicRanges glue httr IRanges jsonlite lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl R6 Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys vctrs XML XVector yaml

Nucleosome Positioning

Rendered fromRJMCMCNucleosomes.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 coverage	plotNucleosomes
A post-treatment function to merge closely positioned nucleosomes, from the same chromosome, identified by the 'rjmcmc' function.	postTreatment
Formated output of predicted nucleosomes	print.rjmcmcNucleosomes
Formated output of predicted nucleosomes	print.rjmcmcNucleosomesBeforeAndAfterPostTreatment
Formated output of predicted nucleosomes	print.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 segment	rjmcmc
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 chromosome	rjmcmcCHR
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