segmentSeq
Bioc currentMethods for identifying small RNA loci from high-throughput sequencing data
Release Lineage
Entered 2.6 · Apr 23, 2010
Current · Requires R 4.6
Description
High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
69 0 exported
Complexity
9.4 avg / 40 max
Call network
69 nodes / 90 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
7,592
Files
69
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
18
Internal functions
47
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
7.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.0.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
33
First release
2010-04-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
9
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 30includes a package overview page
- Examples that run
- 100%15 run in a plain check
- Exported functions with examples
- 63%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 13%
Repository practices
Checks run against github.com/samgg/segmentseq on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
Topics
People
- Samuel Granjeaud maintainer
- Thomas J. Hardcastle author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("segmentSeq")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.