R Observatory: Metrics for signifinder version 1.13.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

signifinder

Bioc current

Collection and implementation of public transcriptional cancer signatures

v1.13.0 · software · AGPL-3

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.16 · Nov 2, 2022

Current · Requires R 4.6

1.0 In 8 of 49 releases 3.23

Description

signifinder is an R package for computing and exploring a compendium of tumor signatures. It allows to compute a variety of signatures coming from public literature, based on gene expression values, and return single-sample (-cell/-spot) scores. Currently, signifinder collects more than 70 distinct signatures, relating to multiple tumors and multiple cancer processes.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

75 58 exported

Complexity

3.6 avg / 20 max

Call network

75 nodes / 202 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

7,658

Files

93

Compiled share

0%

Has compiled src

No

Language breakdown

R 3,836 (50.1%)Tests 782 (10.2%)Docs 2,769 (36.2%)Vignettes 271 (3.5%)

API

Exported functions

58

Internal functions

17

Recent export changes

v3.20+7 CD39CD8TcellSign, SCSubtypeSign, interferonSign +4 more −3 breastStateSign, glioCellStateSign, melStateSign

v3.19+13 ADOSign, APMSign, COXISSign +10 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.20

testthat edition

3

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

9

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.4.0

System requirements

–

C++ standard

–

License

AGPL-3

License flags

SPDX valid, OSI approved

History

Versions

8

First release

2022-11-01

Latest release

2026-04-28

Avg cadence

189 days

Cold removal rate

100%

Dep drift

6

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 110 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Topics

Software › AssayDomain › GeneExpression

Software › BiologicalQuestion › GeneTarget

Software › ResearchField › Immunology › ImmunoOncology

Software › ResearchField › BiomedicalInformatics

Software › Technology › Sequencing › RNASeq

Software › Technology › Microarray

Software › WorkflowStep › ReportWriting

Software › WorkflowStep › Visualization

Software › Technology › SingleCell

Software › Technology › Spatial

Software › BiologicalQuestion › GeneSignaling

People

Stefania Pirrotta maintainer author
Enrica Calura author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("signifinder")

Format

Pirrotta, S., & Calura, E. (2026). signifinder: Collection and implementation of public transcriptional cancer signatures (Version 1.13.0) [Computer software]. https://bioconductor.org/packages/signifinder

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for signifinder version 1.13.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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