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RJMCMCNucleosomes

Bioconductor Package - Genome-Wide Nucleosome Positioning in R with an optimized section in C++

https://github.com/arnauddroitlab/rjmcmcnucleosomes

Science Score: 23.0%

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    Found 4 DOI reference(s) in README
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    Links to: researchgate.net
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    Low similarity (11.0%) to scientific vocabulary

Keywords

bayesian-t-mixture bioconductor c-plus-plus genome-wide-profiling multinomial-dirichlet-prior nucleosome-positioning nucleosomes r reversible-jump-mcmc

Keywords from Contributors

nucleosome-maps simulator synthetic-nucleosomes bioconductor-package r-language copy-number-variation cnv looking-for-maintainer single-cell-rna-seq single-cell
Last synced: 6 months ago · JSON representation

Repository

Bioconductor Package - Genome-Wide Nucleosome Positioning in R with an optimized section in C++

Basic Info
Statistics
  • Stars: 0
  • Watchers: 4
  • Forks: 2
  • Open Issues: 4
  • Releases: 0
Topics
bayesian-t-mixture bioconductor c-plus-plus genome-wide-profiling multinomial-dirichlet-prior nucleosome-positioning nucleosomes r reversible-jump-mcmc
Created over 9 years ago · Last pushed over 8 years ago

https://github.com/ArnaudDroitLab/RJMCMCNucleosomes/blob/master/ 

Genome-Wide Nucleosome Positioning using High-Throughput Short-Read Data (MNase-Seq)
=====================

[![Build Status](https://travis-ci.org/ArnaudDroitLab/RJMCMCNucleosomes.svg?branch=master)](https://travis-ci.org/ArnaudDroitLab/RJMCMCNucleosomes)
[![codecov](https://codecov.io/gh/ArnaudDroitLab/RJMCMCNucleosomes/branch/master/graph/badge.svg)](https://codecov.io/gh/ArnaudDroitLab/RJMCMCNucleosomes)

This package uses informative Multinomial-Dirichlet prior in a t-mixture with 
reversible jump estimation of nucleosome positions for genome-wide profiling.

This package is in R with an optimized section in C++.


## 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


## Bioconductor Package ##

[![Bioconductor Time](http://bioconductor.org/shields/years-in-bioc/RJMCMCNucleosomes.svg)](http://bioconductor.org/packages/release/bioc/html/RJMCMCNucleosomes "Bioconductor status")

_RJMCMCNucleosomes_ is now an official package of [Bioconductor](http://bioconductor.org/). The current release can be directly downloaded from their website:
[Current release](http://bioconductor.org/packages/RJMCMCNucleosomes/)


## Notes ##

To use this current _RJMCMCNucleosomes_ version, the use of the Rcpp package is mandatory. This implies having GSL library installed.


## Authors ##

[Pascal Belleau](http://ca.linkedin.com/in/pascalbelleau 
"Pascal Belleau"),
[Rawane Samb](https://ca.linkedin.com/in/rawanesamb "Rawane Samb"), 
[Astrid Deschênes](http://ca.linkedin.com/in/astriddeschenes 
"Astrid Deschênes"), 
[Khader Khadraoui](http://archimede.mat.ulaval.ca/pages/khaderk/ "Khader Khadraoui"), 
[Lajmi Lakhal-Chaieb](https://www.researchgate.net/profile/Lajmi_Lakhal-Chaieb "Lajmi Lakhal-Chaieb")
and [Arnaud Droit](http://ca.linkedin.com/in/drarnaud "Arnaud Droit").

See [AD Lab](http://compbio.ulaval.ca/ "AD Lab") website.


## Maintainer ##

[Astrid Deschênes](http://ca.linkedin.com/in/astriddeschenes 
"Astrid Deschênes")


## License ##

This package and the underlying _RJMCMCNucleosomes_ 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](http://opensource.org/licenses/Artistic-2.0)


## Bugs/Feature requests ##

If you have any bugs or feature requests, [let us know](https://github.com/ArnaudDroitLab/RJMCMCNucleosomes/issues). 

Thanks!

Owner

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

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 623
  • Total Committers: 10
  • Avg Commits per committer: 62.3
  • Development Distribution Score (DDS): 0.308
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 431
Astrid Deschenes a****n 86
belleau p****u@h****m 75
belleau b****u@P****l 9
Astrid Louise Deschenes A****s@c****a 8
a.deschenes a****s@b****8 7
samraw01 r****a@g****m 3
Herve Pages h****s@f****g 2
mtmorgan@fhcrc.org m****n@f****g@b****8 1
Martin Morgan m****n@f****g 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 3 crchudequebec.ulaval.ca: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 13
  • Total pull requests: 45
  • Average time to close issues: 18 days
  • Average time to close pull requests: 25 minutes
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.38
  • Average comments per pull request: 0.47
  • Merged pull requests: 44
  • 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
View more stats
Top Authors
Issue Authors
  • adeschen (12)
Pull Request Authors
  • adeschen (23)
  • belleau (22)
Top Labels
Issue Labels
enhancement (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 11,213 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
bioconductor.org: RJMCMCNucleosomes

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

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 11,213 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 20.3%
Downloads: 60.9%
Maintainers (1)
adeschen@hotmail.com
Last synced: about 1 year ago

Dependencies

DESCRIPTION cran
  • GenomicRanges * depends
  • IRanges * depends
  • R >= 3.4 depends
  • BiocGenerics * imports
  • BiocParallel * imports
  • GenomeInfoDb * imports
  • Rcpp >= 0.12.5 imports
  • S4Vectors * imports
  • consensusSeekeR * imports
  • grDevices * imports
  • graphics * imports
  • methods * imports
  • stats * imports
  • BiocStyle * suggests
  • RUnit * suggests
  • knitr * suggests
  • nucleoSim * suggests
  • rmarkdown * suggests