# -------------------------------------------- # CITATION file created with {cffr} R package # See also: https://docs.ropensci.org/cffr/ # -------------------------------------------- cff-version: 1.2.0 message: 'To cite package "scPairs" in publications use:' type: software license: MIT title: 'scPairs: Identifying Synergistic Gene Pairs in Single-Cell and Spatial Transcriptomics' version: 0.1.9 doi: 10.32614/CRAN.package.scPairs abstract: 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 . authors: - family-names: Wang given-names: Zhaoqing email: zhaoqingwang@mail.sdu.edu.cn orcid: https://orcid.org/0000-0001-8348-7245 repository: https://zhaoqing-wang.r-universe.dev repository-code: https://github.com/zhaoqing-wang/scPairs commit: 34ad4a7b3fd3108a7375ac65a27bd335ae7a774f url: https://github.com/zhaoqing-wang/scPairs date-released: '2026-04-23' contact: - family-names: Wang given-names: Zhaoqing email: zhaoqingwang@mail.sdu.edu.cn orcid: https://orcid.org/0000-0001-8348-7245