RegionalST
Bioc currentInvestigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data
Release Lineage
Entered 3.18 · Oct 25, 2023
Current · Requires R 4.6
Description
This package analyze spatial transcriptomics data through cross-regional cell type-specific analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
29 16 exported
Complexity
3.7 avg / 12 max
Call network
29 nodes / 28 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
3,287
Files
66
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
16
Internal functions
13
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.04
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
63
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
6
First release
2023-12-01
Latest release
2026-04-28
Avg cadence
181 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
- 21
- Examples that run
- 90%19 run in a plain check · 2 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 14%
- RegionalST HTML
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| exampleRes | list | 3 elements | No other package |
| example_sce | – | – | – |
| pathways_hallmark | list | 50 elements | No other package |
| pathways_kegg | list | 186 elements | No other package |
| pathways_reactome | list | 1,635 elements | No other package |
Topics
People
- Ziyi Li author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("RegionalST")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.