clustSIGNAL
Bioc currentClustSIGNAL: a spatial clustering method
Release Lineage
Entered 3.21 · Apr 16, 2025
Current · Requires R 4.6
Description
clustSIGNAL: clustering of Spatially Informed Gene expression with Neighbourhood Adapted Learning. A tool for adaptively smoothing and clustering gene expression data. clustSIGNAL uses entropy to measure heterogeneity of cell neighbourhoods and performs a weighted, adaptive smoothing, where homogeneous neighbourhoods are smoothed more and heterogeneous neighbourhoods are smoothed less. This not only overcomes data sparsity but also incorporates spatial context into the gene expression data. The resulting smoothed gene expression data is used for clustering and could be used for other downstream analyses.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
13 6 exported
Complexity
4.3 avg / 15 max
Call network
13 nodes / 8 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
2,116
Files
36
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
6
Internal functions
7
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.05
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
4.4.0
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
3
First release
2025-04-15
Latest release
2026-09-09
Avg cadence
256 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
- 16 (7 internal)
- Examples that run
- 100%6 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 75%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- ClustSIGNAL tutorial HTML
- Bug fix: corrected a bug in the vignette where ARI() gives error if given a regular vector without factors.
From NEWS.md in the release
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/sydneybiox/clustsignal on 2026-10-21.
GitHub Pages site last deployed 2026-09-09 · The repository has a site deploy workflow
pkgdown site last built 2026-09-09
Datasets
Topics
People
- Pratibha Panwar maintainer author contributor
- Shila Ghazanfar author contributor
- Boyi Guo author
- Stephanie Hicks author
- Haowen Zhao author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("clustSIGNAL")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.