biscuiteer
Bioc currentConvenience Functions for Biscuit
Release Lineage
Entered 3.10 · Oct 30, 2019
Current · Requires R 4.6
Description
A test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
47 27 exported
Complexity
4 avg / 29 max
Call network
47 nodes / 30 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
4,944
Files
114
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
27
Internal functions
20
Testing
Has tests
Yes
Test-to-code ratio
0.01
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
14
First release
2019-10-29
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
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
- 44includes a package overview page
- Examples that run
- 100%27 run in a plain check
- Exported functions with examples
- 96%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/trichelab/biscuiteer on 2026-10-11.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| ENSR_subset.hg19 | – | – | – |
| ENSR_subset.hg38 | – | – | – |
| GRCh37.chromArm | – | – | – |
| GRCh38.chromArm | – | – | – |
| H9state23unmeth.hg19 | – | – | – |
| H9state23unmeth.hg38 | – | – | – |
| HMM_CpG_islands.hg19 | – | – | – |
| HMM_CpG_islands.hg38 | – | – | – |
| clocks | data.frame | 730 × 14 | No other package |
| hg19.chromArm | – | – | – |
| hg38.chromArm | – | – | – |
| seqinfo.hg19 | – | – | – |
| seqinfo.hg38 | – | – | – |
| seqinfo.mm10 | – | – | – |
Topics
People
- Jacob Morrison author maintainer
- James Eapen author
- Lyong Heo author
- Benjamin Johnson author
- Tim Triche author
- Wanding Zhou author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("biscuiteer")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.