nnSVG
Bioc currentScalable identification of spatially variable genes in spatially-resolved transcriptomics data
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more spatial locations.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
2 2 exported
Complexity
7.5 avg / 12 max
Call network
2 nodes / 0 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
1,462
Files
14
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
2
Internal functions
0
Testing
Has tests
Yes
Test-to-code ratio
0.09
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-07-18
Latest release
2026-07-14
Avg cadence
207 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 2
- Examples that run
- 100%2 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- nnSVG Tutorial HTML
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/lmweber/nnsvg on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Topics
Depended on by (2)
People
- Lukas M. Weber author maintainer
- Stephanie C. Hicks author
Cite
Cite this package
Run in R for the authors' entry:
citation("nnSVG")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/s41467-023-39748-z.
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.