Package: scPairs
Version: 0.1.9
Title: 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>.
Authors@R: 
    person(given = "Zhaoqing", family = "Wang",
           email = "zhaoqingwang@mail.sdu.edu.cn",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-8348-7245"))
License: MIT + file LICENSE
URL: https://github.com/zhaoqing-wang/scPairs
BugReports: https://github.com/zhaoqing-wang/scPairs/issues
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)
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Date: 2026-04-23
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libicu-dev libpng-dev libuv1-dev libxml2-dev
        libssl-dev python3 zlib1g-dev
Repository: https://zhaoqing-wang.r-universe.dev
Date/Publication: 2026-04-23 12:29:49 UTC
RemoteUrl: https://github.com/zhaoqing-wang/scpairs
RemoteRef: HEAD
RemoteSha: 34ad4a7b3fd3108a7375ac65a27bd335ae7a774f
NeedsCompilation: no
Packaged: 2026-07-22 08:13:29 UTC; root
Author: Zhaoqing Wang [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8348-7245>)
Maintainer: Zhaoqing Wang <zhaoqingwang@mail.sdu.edu.cn>