casper
Bioc currentCharacterization of Alternative Splicing Based on Paired-End Reads
Release Lineage
Entered 2.12 · Apr 4, 2013
Current · Requires R 4.6
Description
Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
503 18 exported
Complexity
5.3 avg / 41 max
Call network
503 nodes / 523 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
26,246
Files
131
Compiled share
54.7%
Has compiled src
Yes
Language breakdown
API
Exported functions
40
Internal functions
110
Testing
Has tests
No
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
2
Dep constraint coverage
10%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6.0
System requirements
–
C++ standard
–
License
GPL (>=2)
License flags
not SPDX, not OSI
History
Versions
27
First release
2013-07-11
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
11
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 44
- Examples that run
- 55%23 run in a plain check · 19 hold no code
- Exported functions with examples
- 94%
- Documented parameters
- 99%
- Return-value docs
- 91%
- Help pages citing references
- 23%
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 |
|---|---|---|---|
| K562.r1l1 | list | 12 elements | No other package |
| distrsGSE37704 | list | 6 elements | No other package |
| hg19DB | – | – | – |
Topics
People
- David Rossell author maintainer
- Manuel Kroiss author
- Victor Pena author
- Camille Stephan-Otto author
- Miranda Stobbe author
Cite
Cite this package
Run in R for the authors' entry:
citation("casper")The package provides a citation file, so citation() returns the authors' own entry.
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.