fgsea
Bioc currentFast Gene Set Enrichment Analysis
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
110 23 exported
Complexity
3 avg / 10 max
Call network
110 nodes / 81 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
7,903
Files
97
Compiled share
24.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
23
Internal functions
26
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.35
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
9.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
MIT + file LICENCE
License flags
SPDX valid, OSI approved
History
Versions
20
First release
2016-11-20
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 30
- Examples that run
- 94%17 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 78%
- Documented parameters
- 100%
- Return-value docs
- 91%
- Help pages citing references
- 0%
Repository practices
5 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/alserglab/fgsea on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| GDS289 | data.frame | 10,000 × 7 | No other package |
| exampleExpressionMatrix | matrix | 10,000 × 12 | No other package |
| examplePathways | list | 1,457 elements | No other package |
| exampleRanks | vector | 12,000 elements | No other package |
| fgsea_res | data.frame | 586 × 7 | No other package |
| gse14308_expression_matrix | data.frame | 10,000 × 12 | No other package |
| pathway | data.frame | 198 × 1 | No other package |
Topics
Depended on by (44)
Show 63 packagesHide 63 packages
Bioconductor (41)
People
- Alexey Sergushichev author maintainer
- Nikolay Budin contributor
- Nikita Golikov author
- Nikita Gusak contributor
- Gennady Korotkevich author
- Zieman Mark contributor
- Vladimir Sukhov author
Cite
Cite this package
Run in R for the authors' entry:
citation("fgsea")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1101/060012.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.