Package: RJMCMCNucleosomes 1.29.0
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:
RJMCMCNucleosomes_1.29.0.tar.gz
RJMCMCNucleosomes_1.29.0.zip(r-4.5)RJMCMCNucleosomes_1.29.0.zip(r-4.4)RJMCMCNucleosomes_1.29.0.zip(r-4.3)
RJMCMCNucleosomes_1.29.0.tgz(r-4.4-arm64)RJMCMCNucleosomes_1.29.0.tgz(r-4.4-x86_64)RJMCMCNucleosomes_1.29.0.tgz(r-4.3-arm64)RJMCMCNucleosomes_1.29.0.tgz(r-4.3-x86_64)
RJMCMCNucleosomes_1.29.0.tar.gz(r-4.5-noble)RJMCMCNucleosomes_1.29.0.tar.gz(r-4.4-noble)
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
- RJMCMC_result - Nucleosomes obtained by running RJMCMC function using reads from reads_demo_02 dataset (for demo purpose).
- 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).
- syntheticNucleosomeReads - Simulated dataset of reads generated by 'nucleoSim' package (for demo purpose).
On BioConductor:RJMCMCNucleosomes-1.29.0(bioc 3.20)RJMCMCNucleosomes-1.28.0(bioc 3.19)
Last updated 2 months agofrom:46dc35f47d
Exports:mergeAllRDSFilesFromDirectorymergeRDSFilesplotNucleosomespostTreatmentrjmcmcrjmcmcCHRsegmentation
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsclicodetoolsconsensusSeekeRcpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslR6RcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzlibbioc