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nucleosim

Bioconductor Package - Simulate synthetic nucleosome maps

https://github.com/arnauddroitlab/nucleosim

Science Score: 13.0%

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    Found 8 DOI reference(s) in README
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    Low similarity (11.7%) to scientific vocabulary

Keywords

bioconductor nucleosome-maps nucleosomes r simulation simulator synthetic-nucleosomes

Keywords from Contributors

bioconductor-package hdf5 rhdf5 derfinder rnaseq core-package deseq2 bioinformatics junction illumina
Last synced: 6 months ago · JSON representation

Repository

Bioconductor Package - Simulate synthetic nucleosome maps

Basic Info
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Topics
bioconductor nucleosome-maps nucleosomes r simulation simulator synthetic-nucleosomes
Created over 10 years ago · Last pushed almost 4 years ago
Metadata Files
Readme

README.md

nucleoSim: Generate synthetic nucleosome maps

R-CMD-check-bio codecov License: Artistic-2.0

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

Bioconductor Time

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!

Owner

  • Name: AD Lab
  • Login: ArnaudDroitLab
  • Kind: organization
  • Location: Quebec City

GitHub Events

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Last Year

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 187
  • Total Committers: 14
  • Avg Commits per committer: 13.357
  • Development Distribution Score (DDS): 0.326
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
adeschen a****n@h****m 126
Astrid Deschenes a****n 14
Nitesh Turaga n****a@g****m 12
Herve Pages h****s@f****g 6
vobencha v****n@r****g 4
Dan Tenenbaum d****a@f****g 4
Hervé Pagès h****s@f****g 4
d.tenenbaum d****m@b****8 4
Astrid Louise Deschenes A****s@c****a 4
vobencha v****a@g****m 4
hpages@fhcrc.org h****s@f****g@b****8 2
Martin Morgan m****n@f****g 1
Pascal Belleau p****u@h****m 1
mtmorgan@fhcrc.org m****n@f****g@b****8 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 5 crchudequebec.ulaval.ca: 1 fredhutch.org: 1 roswellpark.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 8 minutes
  • Total issue authors: 0
  • Total pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.5
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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  • adeschen (1)
  • belleau (1)
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Dependencies

DESCRIPTION cran
  • IRanges * imports
  • S4Vectors * imports
  • graphics * imports
  • methods * imports
  • stats * imports
  • BiocGenerics * suggests
  • BiocStyle * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests