GenomicFeatures
Bioc currentQuery the gene models of a given organism/assembly
Release Lineage
Entered 2.5 · Oct 28, 2009
Current · Requires R 4.6
Description
Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
169 12 exported
Complexity
2.9 avg / 20 max
Call network
169 nodes / 194 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
8,883
Files
82
Compiled share
2.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
36
Internal functions
143
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
61.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
34
First release
2009-10-27
Latest release
2026-04-28
Avg cadence
185 days
Cold removal rate
100%
Dep drift
28
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 23
- Examples that run
- 100%22 run in a plain check
- Exported functions with examples
- 94%
- Documented parameters
- 88%
- Return-value docs
- 100%
- Help pages citing references
- 0%
DEPRECATED AND DEFUNCT
- After they got formally deprecated in GenomicFeatures in BioC 3.21 and defunct in BioC 3.22, all the functions that went to txdbmaker in BioC 3.19 are now gone for good.
- After being defunct in BioC 3.22, microRNAs() is now gone for good.
From NEWS in the release
Repository practices
Checks run against github.com/bioconductor/genomicfeatures on 2026-10-18.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| cD.exByEdge | matrix | 6,885 × 6 | No other package |
| cD.exsByGenes | matrix | 14,262 × 6 | No other package |
| events | vector | 60 elements | No other package |
| sample_ranges | – | – | – |
Topics
Depended on by (243)
Show 64 packagesHide 64 packages
Bioconductor (239)
CRAN (4)
Suggested by (84)
People
- H. Pagès author maintainer
- P. Aboyoun author
- S. Arora contributor
- M. Carlson author
- S. Falcon author
- M. Lawrence author
- J. MacDonald contributor
- M. Morgan author
- V. Obenchain author
- M. Ramos contributor
- S. Saini contributor
- D. Sarkar author
- P. Shannon contributor
- L. Shepherd contributor
- D. Tenenbaum contributor
- D. Van Twisk contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("GenomicFeatures")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 v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.