segmenter
Bioc currentPerform Chromatin Segmentation Analysis in R by Calling ChromHMM
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
Chromatin segmentation analysis transforms ChIP-seq data into signals over the genome. The latter represents the observed states in a multivariate Markov model to predict the chromatin's underlying states. ChromHMM, written in Java, integrates histone modification datasets to learn the chromatin states de-novo. The goal of this package is to call chromHMM from within R, capture the output files in an S4 object and interface to other relevant Bioconductor analysis tools. In addition, segmenter provides functions to test, select and visualize the output of the segmentation.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
31 25 exported
Complexity
2.2 avg / 7 max
Call network
31 nodes / 22 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
4,123
Files
66
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
38
Internal functions
6
Testing
Has tests
Yes
Test-to-code ratio
0.28
testthat edition
–
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
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2021-10-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 36
- Examples that run
- 100%26 run in a plain check
- Exported functions with examples
- 96%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
2 development-tooling and community-health practices detected across 1 family in the upstream repository
Checks run against github.com/mahshaaban/segmenter on 2026-10-18.
The R CMD check workflow runs on Linux
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| GM12878_chr11_binary | – | – | – |
| K562_chr11_binary | – | – | – |
| cell_mark_table | data.frame | 3 × 3 | No other package |
| test_obj | – | – | – |
| test_objs | list | 6 elements | No other package |
Topics
People
- Mahmoud Ahmed author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("segmenter")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
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