RJMCMCNucleosomes
Bioc currentBayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
Release Lineage
Entered 3.5 · Apr 25, 2017
Current · Requires R 4.6
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
116 7 exported
Complexity
6 avg / 22 max
Call network
116 nodes / 22 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
7,313
Files
81
Compiled share
44.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
7
Internal functions
13
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
16.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5
System requirements
1 externalRcpp
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
19
First release
2017-04-24
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 25 (10 internal)includes a package overview page
- Examples that run
- 100%23 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
2 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/arnauddroitlab/rjmcmcnucleosomes on 2026-10-21.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| RJMCMC_result | rjmcmcNucleosomes | 4 elements | No other package |
| RJMCMC_seg_01 | rjmcmcNucleosomes | 4 elements | No other package |
| RJMCMC_seg_02 | rjmcmcNucleosomes | 4 elements | No other package |
| RJMCMC_seg_03 | rjmcmcNucleosomes | 4 elements | No other package |
| reads_demo_01 | – | – | – |
| reads_demo_02 | – | – | – |
| segmentResult_1 | rjmcmcNucleosomes | 4 elements | No other package |
| segmentResult_10 | rjmcmcNucleosomes | 4 elements | No other package |
| segmentResult_11 | rjmcmcNucleosomes | 4 elements | No other package |
| segmentResult_2 | rjmcmcNucleosomes | 4 elements | No other package |
| segmentResult_3 | rjmcmcNucleosomes | 4 elements | No other package |
| segmentResult_4 | rjmcmcNucleosomes | 4 elements | No other package |
| segmentResult_5 | rjmcmcNucleosomes | 4 elements | No other package |
| segmentResult_6 | rjmcmcNucleosomes | 4 elements | No other package |
| segmentResult_7 | rjmcmcNucleosomes | 4 elements | No other package |
| segmentResult_8 | rjmcmcNucleosomes | 4 elements | No other package |
| segmentResult_9 | rjmcmcNucleosomes | 4 elements | No other package |
| syntheticNucleosomeReads | syntheticNucReads | 6 elements | No other package |
Topics
People
- Astrid Deschênes maintainer author
- Pascal Belleau author
- Arnaud Droit author
- Khader Khadraoui author
- Lajmi Lakhal-Chaieb author
- Rawane Samb author
Cite
Cite this package
Run in R for the authors' entry:
citation("RJMCMCNucleosomes")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1515/sagmb-2014-0098.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.