concordexR
Bioc currentIdentify Spatial Homogeneous Regions with concordex
Release Lineage
Entered 3.17 · Apr 26, 2023
Current · Requires R 4.6
Description
Spatial homogeneous regions (SHRs) in tissues are domains that are homogenous with respect to cell type composition. We present a method for identifying SHRs using spatial transcriptomics data, and demonstrate that it is efficient and effective at finding SHRs for a wide variety of tissue types. concordex relies on analysis of k-nearest-neighbor (kNN) graphs. The tool is also useful for analysis of non-spatial transcriptomics data, and can elucidate the extent of concordance between partitions of cells derived from clustering algorithms, and transcriptomic similarity as represented in kNN graphs.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
20 0 exported
Complexity
3.3 avg / 9 max
Call network
20 nodes / 10 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
1,267
Files
28
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
2
Internal functions
19
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.21
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
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
4.5.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
7
First release
2023-04-25
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
11
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 50%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Kayla Jackson author maintainer
- A. Sina Booeshaghi author
- Angel Galvez-Merchan author
- Alexandra Kim contributor
- Laura Luebbert contributor
- Lambda Moses author
- Lior Pachter author rev ths
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("concordexR")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.