hoodscanR
Bioc currentSpatial cellular neighbourhood scanning in R
Release Lineage
Entered 3.18 · Oct 25, 2023
Current · Requires R 4.6
Description
hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
28 8 exported
Complexity
3.3 avg / 16 max
Call network
28 nodes / 17 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
2,511
Files
50
Compiled share
3.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
12
Internal functions
17
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.17
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
6.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
6
First release
2023-10-24
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
- 14 (2 internal)includes a package overview page
- Examples that run
- 100%13 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 96%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/davislaboratory/hoodscanr on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2025-11-12 · The repository has a site deploy workflow
pkgdown site last built 2025-11-12
Datasets
Topics
Depended on by (1)
Bioconductor (1)
People
- Ning Liu author maintainer
- Jarryd Martin author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("hoodscanR")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.