sparrow
Bioc currentTake command of set enrichment analyses through a unified interface
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
198 57 exported
Complexity
5.3 avg / 63 max
Call network
198 nodes / 188 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
17,900
Files
206
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
61
Internal functions
132
Testing
Has tests
Yes
Test-to-code ratio
0.24
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
30%
Unsafe pattern score
0
Dep constraint coverage
27.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2022-03-23
Latest release
2026-04-28
Avg cadence
181 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
- 59
- Examples that run
- 89%49 run in a plain check · 6 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 100%
- Documented parameters
- 94%
- Return-value docs
- 100%
- Help pages citing references
- 3%
Repository practices
8 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/lianos/sparrow on 2026-10-21.
The R CMD check workflow runs on Linux
GitHub Pages site last deployed 2026-10-21 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| TCGA-BRCA-some.DGEList | DGEList | 3 elements | No other package |
| custom-sigs | data.frame | 113 × 4 | No other package |
| dataframe-input-short | data.frame | 837 × 10 | No other package |
| genesets-sparrow-list-of-lists | list | 3 elements | No other package |
| gsea-methods | data.frame | 11 × 6 | No other package |
| species-info | – | – | – |
| test-SparrowResult | – | – | – |
Topics
Suggested by (1)
People
- Steve Lianoglou author maintainer
-
Aratus Informatics, LLC
funder
2023+
-
Denali Therapeutics
funder
2018-2022
-
Genentech
funder
2014 - 2017
- Arkadiusz Gladki contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("sparrow")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
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.