GenomicRanges
Bioc currentRepresentation and manipulation of genomic intervals
Release Lineage
Entered 2.6 · Apr 23, 2010
Current · Requires R 4.6
Description
The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
158 23 exported
Complexity
3.8 avg / 27 max
Call network
158 nodes / 106 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
15,757
Files
83
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
30
Internal functions
124
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
93.3%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
50%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
33
First release
2010-08-28
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
94.9%
Dep drift
10
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 25
- Examples that run
- 96%22 run in a plain check · 1 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- 66%
- Return-value docs
- 73%
- Help pages citing references
- 8%
SIGNIFICANT USER-VISIBLE CHANGES
- The package no longer contains C code.
- Replace rtracklayer with UCSC.utils in the Suggests field.
- Use TxDb.Athaliana.BioMart.plantsmart51 instead of TxDb.Athaliana.BioMart.plantsmart22 in vignette.
BUG FIXES
- Fix small bug in restrict() method for GenomicRanges object.
From NEWS in the release
Repository practices
Checks run against github.com/bioconductor/genomicranges on 2026-10-11.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| feature_frags | data.frame | 3 × 6 | No other package |
Topics
Depended on by (810)
Show 90 packagesHide 90 packages
Bioconductor (775)
CRAN (35)
Suggested by (90)
People
- Hervé Pagès author maintainer
- Patrick Aboyoun author
- Sonali Arora contributor
- Michael Lawrence author
- Martin Morgan contributor
- Kayla Morrell contributor
- Valerie Obenchain contributor
- Marcel Ramos contributor
- Lori Shepherd contributor
- Dan Tenenbaum contributor
- Daniel van Twisk contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("GenomicRanges")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1371/journal.pcbi.1003118.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.