sSNAPPY
Bioc currentSingle Sample directioNAl Pathway Perturbation analYsis
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
A single sample pathway perturbation testing method for RNA-seq data. The method propagates changes in gene expression down gene-set topologies to compute single-sample directional pathway perturbation scores that reflect potential direction of change. Perturbation scores can be used to test significance of pathway perturbation at both individual-sample and treatment levels.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
17 8 exported
Complexity
4.4 avg / 11 max
Call network
17 nodes / 10 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
4,202
Files
51
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
10
Internal functions
9
Testing
Has tests
Yes
Test-to-code ratio
0.33
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
1 externalC++11
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-08-03
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
12
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 15 (1 internal)includes a package overview page
- Examples that run
- 80%8 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 93%
- Return-value docs
- 90%
- Help pages citing references
- 27%
Repository practices
7 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/wenjun-liu/ssnappy on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2023-11-01 · The repository has a site deploy workflow
pkgdown site last built 2023-11-01
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| entrez2name | tibble | 25,699 × 2 | No other package |
| gsAnnotation_df | tibble | 549 × 2 | No other package |
| gsAnnotation_df_reactome | tibble | 2,647 × 2 | No other package |
| gsTopology | list | 315 elements | No other package |
| logCPM_example | matrix | 7,672 × 15 | No other package |
| metadata_example | tibble | 15 × 4 | No other package |
| normalisedScores | data.frame | 2,140 × 8 | No other package |
| permutedScore | list | 313 elements | No other package |
Topics
People
- Wenjun Liu author maintainer
- Stephen Pederson author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("sSNAPPY")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 v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.