spicyR
Bioc currentSpatial analysis of in situ cytometry data
Release Lineage
Entered 3.11 · Apr 28, 2020
Current · Requires R 4.6
Description
The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
36 10 exported
Complexity
6 avg / 38 max
Call network
36 nodes / 23 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
3,700
Files
39
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
11
Internal functions
20
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.03
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
4.1
System requirements
–
C++ standard
–
License
GPL (>=2)
License flags
not SPDX, not OSI
History
Versions
13
First release
2020-07-10
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
34
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 14
- Examples that run
- 91%10 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/sydneybiox/spicyr on 2026-10-22.
GitHub Pages site last deployed 2026-10-22 · The repository has a site deploy workflow
pkgdown site last built 2026-02-24
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| diabetesData | – | – | – |
| isletCells | data.frame | 4,650 × 75 | No other package |
| spicyTest | SpicyResults | 13 elements | No other package |
Topics
Depended on by (2)
Suggested by (2)
People
- Ellis Patrick author maintainer
- Farhan Ameen contributor
- Nicolas Canete author
- Alex Qin contributor
- Shreya Rao contributor
- Nicholas Robertson contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("spicyR")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.