scmeth
Bioc currentFunctions to conduct quality control analysis in methylation data
Release Lineage
Entered 3.7 · May 1, 2018
Current · Requires R 4.6
Description
Functions to analyze methylation data can be found here. Some functions are relevant for single cell methylation data but most other functions can be used for any methylation data. Highlight of this workflow is the comprehensive quality control report.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
12 12 exported
Complexity
2.2 avg / 5 max
Call network
12 nodes / 0 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
1,247
Files
46
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
12
Internal functions
0
Recent export changes
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
0
Dep constraint coverage
18.8%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
17
First release
2018-06-01
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
8
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 13includes a package overview page
- Examples that run
- 100%12 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Vignette Title HTML
Repository practices
2 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/aryeelab/scmeth on 2026-10-11.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| 16_trimmed_sorted | data.frame | 300 × 5 | No other package |
| 2017-04-21_HG23KBCXY_2_AGGCAGAA_TATCTC_pe.M-bias | – | – | – |
| bs | – | – | – |
| sc-RRBS-zygote_01.bsConv | – | – | – |
| sc-RRBS-zygote_01.read_metrics | – | – | – |
| sc-RRBS-zygote_02.bsConv | – | – | – |
| sc-RRBS-zygote_02.read_metrics | – | – | – |
| sc-RRBS-zygote_03.bsConv | – | – | – |
| sc-RRBS-zygote_03.read_metrics | – | – | – |
| se | – | – | – |
Topics
Suggested by (1)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("scmeth")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.