airway
Bioc currentRangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014
Release Lineage
Entered 3.0 · Oct 14, 2014
Current · Requires R 4.6
Description
This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. 'RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.' PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778.
None published for Bioconductor
Call graph
Open call graph →Code intelligence has not been computed for this package yet.
Code
Structure
Lines of code
274
Files
48
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
0
Internal functions
0
Testing
Has tests
No
Test-to-code ratio
–
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
LGPL
License flags
not SPDX, not OSI
History
Versions
24
First release
2014-12-02
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 2
- Examples that run
- no examples
- Exported functions with examples
- not tracked
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 100%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| GSE52778_series_matrix | – | – | – |
| SraRunInfo_SRP033351 | data.frame | 16 × 46 | No other package |
| airway | – | – | – |
| gse | – | – | – |
| sample_table | data.frame | 8 × 10 | No other package |
Topics
Depended on by (4)
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Bioconductor (4)
Suggested by (56)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("airway")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.