scPairs: Identifying Synergistic Gene Pairs in Single-Cell and Spatial Transcriptomics

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>.

Version:	0.1.8
Depends:	R (≥ 4.1.0)
Imports:	data.table, ggplot2, ggraph, ggrepel, igraph, methods, Matrix, patchwork, Seurat (≥ 4.0), SeuratObject, stats, tidygraph, tidyr
Suggests:	AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, crayon, ggExtra, RANN, testthat (≥ 3.0.0)
Published:	2026-03-05
DOI:	10.32614/CRAN.package.scPairs (may not be active yet)
Author:	Zhaoqing Wang [aut, cre]
Maintainer:	Zhaoqing Wang <zhaoqingwang at mail.sdu.edu.cn>
BugReports:	https://github.com/zhaoqing-wang/scPairs/issues
License:	MIT + file LICENSE
URL:	https://github.com/zhaoqing-wang/scPairs
NeedsCompilation:	no
Materials:	README, NEWS
CRAN checks:	scPairs results

Documentation:

Reference manual:

scPairs.html , scPairs.pdf

Downloads:

Package source:	scPairs_0.1.8.tar.gz
Windows binaries:	r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): scPairs_0.1.8.tgz, r-oldrel (arm64): scPairs_0.1.8.tgz, r-release (x86_64): scPairs_0.1.8.tgz, r-oldrel (x86_64): scPairs_0.1.8.tgz

Linking:

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