tpSVG
Bioc currentThin plate models to detect spatially variable genes
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
The goal of `tpSVG` is to detect and visualize spatial variation in the gene expression for spatially resolved transcriptomics data analysis. Specifically, `tpSVG` introduces a family of count-based models, with generalizable parametric assumptions such as Poisson distribution or negative binomial distribution. In addition, comparing to currently available count-based model for spatially resolved data analysis, the `tpSVG` models improves computational time, and hence greatly improves the applicability of count-based models in SRT data analysis.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
1 1 exported
Complexity
18 avg / 18 max
Call network
1 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
674
Files
12
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
1
Internal functions
0
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.14
testthat edition
3
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
4.4
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
5
First release
2024-04-30
Latest release
2026-04-28
Avg cadence
182 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
- 1
- Examples that run
- 100%1 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 91%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- intro_to_tpSVG HTML
Repository practices
8 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/boyiguo1/tpsvg on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2024-02-28 · The repository has a site deploy workflow
Topics
People
- Boyi Guo author maintainer
- Stephanie C. Hicks author
- Lukas M. Weber contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("tpSVG")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.