nucleoSim
Bioc currentGenerate synthetic nucleosome maps
Release Lineage
Entered 3.3 · May 4, 2016
Current · Requires R 4.6
Description
This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The synthetic hybridization data of “Tiling Arrays” can also be generated. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform. In addition, a visualization tool is provided to explore the synthetic nucleosome maps.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
8 3 exported
Complexity
7.3 avg / 32 max
Call network
8 nodes / 6 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
3,394
Files
26
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
3
Internal functions
5
Testing
Has tests
Yes
Test-to-code ratio
1.40
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
21
First release
2016-05-15
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 9 (3 internal)includes a package overview page
- Examples that run
- 100%8 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
4 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/arnauddroitlab/nucleosim on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows
Topics
Suggested by (1)
People
- Astrid Deschênes maintainer author
- Pascal Belleau author
- Arnaud Droit author
- Rawane Samb author
Cite
Cite this package
Run in R for the authors' entry:
citation("nucleoSim")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1515/sagmb-2014-0098, 10.1093/bioinformatics/btr345.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.