CSAR
Bioc currentStatistical tools for the analysis of ChIP-seq data
Release Lineage
Entered 2.6 · Apr 23, 2010
Current · Requires R 4.6
Description
Statistical tools for ChIP-seq data analysis. The package includes the statistical method described in Kaufmann et al. (2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
16 0 exported
Complexity
4.3 avg / 16 max
Call network
16 nodes / 8 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
1,126
Files
35
Compiled share
1.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
1
Internal functions
0
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.15.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
33
First release
2010-04-22
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
6
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 12includes a package overview page
- Examples that run
- 92%11 run in a plain check · 1 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 92%
- CSAR Vignette PDF
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| TAIR8_genes_test | data.frame | 27 × 9 | No other package |
| controlSEP3_test | data.frame | 1,395 × 5 | No other package |
| sampleSEP3_test | data.frame | 923 × 5 | No other package |
Topics
Depended on by (1)
Bioconductor (1)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("CSAR")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.