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

Description

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(s)

Pascal Belleau, Rawane Samb, Astrid Deschênes, Khader Khadraoui, Lajmi Lakhal and Arnaud Droit

Maintainer: Astrid Deschenes <adeschen@hotmail.com>

See Also

• rjmcmc for profiling of nucleosome positions for a segment

• rjmcmcCHR for profiling of nucleosome positions for a large region. The function will take care of spliting and merging.

• segmentation for spliting a GRanges containing reads in a list of smaller segments for the rjmcmc function.

• postTreatment for merging closely positioned nucleosomes

• mergeRDSFiles for merging nucleosome information from selected RDS files.

• plotNucleosomes for generating a graph containing the nucleosome positions and the read coverage.