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.
None published for Bioconductor
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
1,265
Files
17
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
2
Internal functions
19
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.21
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
4.5.0
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
- Help pages
- 1
- Examples that run
- 100%1 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 50%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- concordex-nonspatial HTML
- overview HTML
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/pachterlab/concordexr on 2026-10-11.
GitHub Pages site last deployed 2025-06-12 · The repository has a site deploy workflow
pkgdown site last built 2025-06-12
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 reviewer thesis advisor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("concordexR")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 v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.