nucleoSim: Generate synthetic nucleosome maps

This nucleoSim package generate synthetic nucleosome maps using parameters given by users. Three different distributions are available: Normal, Student and Uniform.

The package has been largely inspired by the Generating synthetic maps section of the Bioconductor nucleR package (Flores and Orozco, 2011).

Bioconductor Package

nucleoSim is now an official package of Bioconductor. The current release can be directly downloaded from their website: Current release

Citing

If you use this package for a publication, we would ask you to cite the following:

Samb R, Khadraoui K, Belleau P, et al. (2015). “Using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.” Statistical Applications in Genetics and Molecular Biology. Volume 14, Issue 6, Pages 517-532, ISSN (Online) 1544-6115, ISSN (Print) 2194-6302, December 2015, doi: 10.1515/sagmb-2014-0098

Flores O and Orozco M (2011). “nucleR: a package for non-parametric nucleosome positioning.” Bioinformatics, 27, pp. 2149–2150. doi: 10.1093/bioinformatics/btr345

Authors

Rawane Samb, Astrid Deschênes, Pascal Belleau and Arnaud Droit.

See AD Lab website.

Maintainer

Astrid Deschênes

License

This package and the underlying nucleoSim code are distributed under the Artistic license 2.0. You are free to use and redistribute this software.

For more information on Artistic 2.0 License see http://opensource.org/licenses/Artistic-2.0

Bugs/Feature requests

If you have any bugs or feature requests, let us know. Thanks!