scPairs
Identifying Synergistic Gene Pairs in Single-Cell and Spatial Transcriptomics
Description
Discovers synergistic gene pairs in single-cell RNA-seq and spatial transcriptomics data. Unlike conventional pairwise co-expression analyses that rely on a single correlation metric, scPairs integrates 14 complementary metrics across five orthogonal evidence layers to compute a composite synergy score with optional permutation-based significance testing. The five evidence layers span cell-level co-expression (Pearson, Spearman, biweight midcorrelation, mutual information, ratio consistency), neighbourhood-aware smoothing (KNN-smoothed correlation, neighbourhood co-expression, cluster pseudo-bulk, cross-cell-type, neighbourhood synergy), prior biological knowledge (GO/KEGG co-annotation Jaccard, pathway bridge score), trans-cellular interaction, and spatial co-variation (Lee's L, co-location quotient). This multi-scale design enables researchers to move beyond simple co-expression towards a comprehensive characterisation of cooperative gene regulation at transcriptomic and spatial resolution. For more information, see the package documentation at <https://github.com/zhaoqing-wang/scPairs>.
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CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026
package dependencies
Packages required but not available: 'ggraph', 'Seurat', 'tidygraph' Packages suggested but not available for checking: 'AnnotationDbi', 'org.Mm.eg.db', 'org.Hs.eg.db' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 25, 2026
NOTE 13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 10, 2026
package dependencies
Package suggested but not available for checking: ‘org.Mm.eg.db’
ERROR 12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 9, 2026
package dependencies
Package required but not available: ‘Seurat’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package suggested but not available for checking: ‘org.Mm.eg.db’
NOTE 12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
package dependencies
Package suggested but not available for checking: ‘org.Mm.eg.db’
Code & tests
Open call graph →Code intelligence has not been computed for this package yet.
Code
Structure
Lines of code
11,185
Files
139
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
14
Internal functions
69
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.13
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
100%
\dontrun example ratio
33.3%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
Yes
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
7.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-03-05
Latest release
2026-03-05
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.
Dependency Network
Version History
1 trackedR Observatory began tracking this package on Mar 10, 2026; it first appeared on CRAN Mar 5, 2026. Releases before tracking aren’t shown.