SOMNiBUS
Bioc currentSmooth modeling of bisulfite sequencing
Release Lineage
Entered 3.13 · May 20, 2021
Current · Requires R 4.6
Description
This package aims to analyse count-based methylation data on predefined genomic regions, such as those obtained by targeted sequencing, and thus to identify differentially methylated regions (DMRs) that are associated with phenotypes or traits. The method is built a rich flexible model that allows for the effects, on the methylation levels, of multiple covariates to vary smoothly along genomic regions. At the same time, this method also allows for sequencing errors and can adjust for variability in cell type mixture.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
46 14 exported
Complexity
7.7 avg / 30 max
Call network
46 nodes / 94 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
7,315
Files
69
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
14
Internal functions
32
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.38
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
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
4.1.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
11
First release
2021-05-19
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
15
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Kathleen Klein maintainer
- My Intelligent Machines Inc. ctr
- Celia Greenwood ths author
- Simon Laurin-Lemay contributor ctr
- Audrey Lemaçon contributor ctr
- Kaiqiong Zhao author