{
  "_id": "6a607d4d14e95619b75da571",
  "Package": "scPairs",
  "Version": "0.1.9",
  "Title": "Identifying Synergistic Gene Pairs in Single-Cell and Spatial\nTranscriptomics",
  "Description": "Discovers synergistic gene pairs in single-cell RNA-seq\nand spatial transcriptomics data. Unlike conventional pairwise\nco-expression analyses that rely on a single correlation\nmetric, scPairs integrates 14 complementary metrics across five\northogonal evidence layers to compute a composite synergy score\nwith optional permutation-based significance testing. The five\nevidence layers span cell-level co-expression (Pearson,\nSpearman, biweight midcorrelation, mutual information, ratio\nconsistency), neighbourhood-aware smoothing (KNN-smoothed\ncorrelation, neighbourhood co-expression, cluster pseudo-bulk,\ncross-cell-type, neighbourhood synergy), prior biological\nknowledge (GO/KEGG co-annotation Jaccard, pathway bridge\nscore), trans-cellular interaction, and spatial co-variation\n(Lee's L, co-location quotient). This multi-scale design\nenables researchers to move beyond simple co-expression towards\na comprehensive characterisation of cooperative gene regulation\nat transcriptomic and spatial resolution. For more information,\nsee the package documentation at\n<https://github.com/zhaoqing-wang/scPairs>.",
  "Authors@R": "person(given = \"Zhaoqing\", family = \"Wang\",\nemail = \"zhaoqingwang@mail.sdu.edu.cn\",\nrole = c(\"aut\", \"cre\"),\ncomment = 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",
  "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\nlibglpk-dev make libicu-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-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": {
    "Date": "2026-07-22 08:13:29 UTC",
    "User": "root"
  },
  "Author": "Zhaoqing Wang [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-8348-7245>)",
  "Maintainer": "Zhaoqing Wang <zhaoqingwang@mail.sdu.edu.cn>",
  "_user": "zhaoqing-wang",
  "_type": "src",
  "_file": "scPairs_0.1.9.tar.gz",
  "_fileid": "https://r2.ropensci.org/d1bb6472aecf2738436691050e10b14d1ad50626537f7906cf41611fe65c4c4e",
  "_filesize": 311615,
  "_sha256": "d1bb6472aecf2738436691050e10b14d1ad50626537f7906cf41611fe65c4c4e",
  "_expires": "2026-10-30T08:20:27.000Z",
  "_created": "2026-07-22T08:13:29.000Z",
  "_published": "2026-07-22T08:20:29.391Z",
  "_jobs": [
    {
      "job": 88868403538,
      "time": 359,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8522879460"
    },
    {
      "job": 88868403609,
      "time": 347,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8522874503"
    },
    {
      "job": 88868403832,
      "time": 224,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8522841897"
    },
    {
      "job": 88868403562,
      "time": 181,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8522807111"
    },
    {
      "job": 88867308536,
      "time": 320,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8522727902"
    },
    {
      "job": 88868403492,
      "time": 235,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8522826610"
    },
    {
      "job": 88868403551,
      "time": 264,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8522839932"
    },
    {
      "job": 88868403633,
      "time": 253,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8522835014"
    },
    {
      "job": 88868403547,
      "time": 246,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8522832075"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/zhaoqing-wang/actions/runs/29902826427",
  "_status": "success",
  "_upstream": "https://github.com/zhaoqing-wang/scpairs",
  "_commit": {
    "id": "34ad4a7b3fd3108a7375ac65a27bd335ae7a774f",
    "author": "zhaoqing-wang <851091628@qq.com>",
    "committer": "zhaoqing-wang <851091628@qq.com>",
    "message": "20260423 1430 commit\n",
    "time": 1776947389
  },
  "_maintainer": {
    "name": "Zhaoqing Wang",
    "email": "zhaoqingwang@mail.sdu.edu.cn",
    "login": "zhaoqing-wang",
    "linkedin": "in/zhaoqingwang",
    "orcid": "0000-0001-8348-7245",
    "description": "M.D. Student @ SDU | Bioinformatics",
    "uuid": 195407069
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggraph",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "Seurat",
      "version": ">= 4.0",
      "role": "Imports"
    },
    {
      "package": "SeuratObject",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tidygraph",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Suggests"
    },
    {
      "package": "org.Mm.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "crayon",
      "role": "Suggests"
    },
    {
      "package": "ggExtra",
      "role": "Suggests"
    },
    {
      "package": "RANN",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "zhaoqing-wang",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-06",
      "n": 11
    },
    {
      "week": "2026-07",
      "n": 4
    },
    {
      "week": "2026-09",
      "n": 23
    },
    {
      "week": "2026-10",
      "n": 3
    },
    {
      "week": "2026-14",
      "n": 1
    },
    {
      "week": "2026-17",
      "n": 3
    }
  ],
  "_tags": [
    {
      "name": "v0.1.0",
      "date": "2026-02-07"
    },
    {
      "name": "v0.1.4",
      "date": "2026-02-08"
    },
    {
      "name": "v0.1.7",
      "date": "2026-02-23"
    },
    {
      "name": "v0.1.8",
      "date": "2026-02-28"
    },
    {
      "name": "v0.1.9",
      "date": "2026-04-23"
    }
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "zhaoqing-wang",
      "count": 45,
      "uuid": 195407069
    }
  ],
  "_userbio": {
    "uuid": 195407069,
    "type": "user",
    "name": "Zhaoqing Wang",
    "followers": 2,
    "description": "M.D. Student @ SDU | Bioinformatics"
  },
  "_downloads": {
    "count": 313,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/scPairs"
  },
  "_devurl": "https://github.com/zhaoqing-wang/scpairs",
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/scPairs.html",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/zhaoqing-wang/scpairs",
  "_realowner": "zhaoqing-wang",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.8",
      "date": "2026-03-05"
    }
  ],
  "_exports": [
    "AssessGenePair",
    "FindAllPairs",
    "FindGenePairs",
    "PlotBridgeNetwork",
    "PlotPairCrossType",
    "PlotPairDimplot",
    "PlotPairHeatmap",
    "PlotPairNetwork",
    "PlotPairScatter",
    "PlotPairSmoothed",
    "PlotPairSpatial",
    "PlotPairSummary",
    "PlotPairSynergy",
    "PlotPairViolin"
  ],
  "_datasets": [
    {
      "name": "scpairs_testdata",
      "title": "Synthetic Seurat Test Object for scPairs Examples and Tests",
      "object": "scpairs_testdata",
      "class": [
        "Seurat"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "AssessGenePair",
      "title": "Assess the Synergy of a Specific Gene Pair",
      "concept": [
        "Section_1_Discovery"
      ],
      "topics": [
        "AssessGenePair"
      ]
    },
    {
      "page": "FindAllPairs",
      "title": "Discover All Synergistic Gene Pairs",
      "concept": [
        "Section_1_Discovery"
      ],
      "topics": [
        "FindAllPairs"
      ]
    },
    {
      "page": "FindGenePairs",
      "title": "Find Synergistic Partners for a Given Gene",
      "concept": [
        "Section_1_Discovery"
      ],
      "topics": [
        "FindGenePairs"
      ]
    },
    {
      "page": "PlotBridgeNetwork",
      "title": "Plot Bridge Gene Network",
      "concept": [
        "Section_2_Visualization"
      ],
      "topics": [
        "PlotBridgeNetwork"
      ]
    },
    {
      "page": "PlotPairCrossType",
      "title": "Plot Cross-Cell-Type Interaction Heatmap",
      "concept": [
        "Section_2_Visualization"
      ],
      "topics": [
        "PlotPairCrossType"
      ]
    },
    {
      "page": "PlotPairDimplot",
      "title": "Plot Gene Pair Co-Expression on UMAP / Dimensionality Reduction",
      "concept": [
        "Section_2_Visualization"
      ],
      "topics": [
        "PlotPairDimplot"
      ]
    },
    {
      "page": "PlotPairHeatmap",
      "title": "Plot Synergy Score Heatmap",
      "concept": [
        "Section_2_Visualization"
      ],
      "topics": [
        "PlotPairHeatmap"
      ]
    },
    {
      "page": "PlotPairNetwork",
      "title": "Plot Gene Interaction Network",
      "concept": [
        "Section_2_Visualization"
      ],
      "topics": [
        "PlotPairNetwork"
      ]
    },
    {
      "page": "PlotPairScatter",
      "title": "Scatter Plot of Two Genes (Cell-Level)",
      "concept": [
        "Section_2_Visualization"
      ],
      "topics": [
        "PlotPairScatter"
      ]
    },
    {
      "page": "PlotPairSmoothed",
      "title": "Enhanced Co-Expression Visualization with Neighbourhood Smoothing",
      "concept": [
        "Section_2_Visualization"
      ],
      "topics": [
        "PlotPairSmoothed"
      ]
    },
    {
      "page": "PlotPairSpatial",
      "title": "Plot Spatial Co-Expression Map",
      "concept": [
        "Section_2_Visualization"
      ],
      "topics": [
        "PlotPairSpatial"
      ]
    },
    {
      "page": "PlotPairSummary",
      "title": "Comprehensive Synergy Summary Plot",
      "concept": [
        "Section_2_Visualization"
      ],
      "topics": [
        "PlotPairSummary"
      ]
    },
    {
      "page": "PlotPairSynergy",
      "title": "Visualize Synergistic Relationship Between Gene Pairs",
      "concept": [
        "Section_2_Visualization"
      ],
      "topics": [
        "PlotPairSynergy"
      ]
    },
    {
      "page": "PlotPairViolin",
      "title": "Violin Plot of Pair Expression Across Clusters",
      "concept": [
        "Section_2_Visualization"
      ],
      "topics": [
        "PlotPairViolin"
      ]
    },
    {
      "page": "print.scPairs_gene_result",
      "title": "Print method for scPairs_gene_result",
      "topics": [
        "print.scPairs_gene_result"
      ]
    },
    {
      "page": "print.scPairs_pair_result",
      "title": "Print method for scPairs_pair_result",
      "topics": [
        "print.scPairs_pair_result"
      ]
    },
    {
      "page": "print.scPairs_result",
      "title": "Print method for scPairs_result",
      "topics": [
        "print.scPairs_result"
      ]
    },
    {
      "page": "scpairs_testdata",
      "title": "Synthetic Seurat Test Object for scPairs Examples and Tests",
      "concept": [
        "Section_0_Data"
      ],
      "topics": [
        "scpairs_testdata"
      ]
    }
  ],
  "_readme": "https://github.com/zhaoqing-wang/scpairs/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "base64enc",
    "BH",
    "bitops",
    "bslib",
    "cachem",
    "caTools",
    "cli",
    "cluster",
    "codetools",
    "commonmark",
    "cowplot",
    "cpp11",
    "crosstalk",
    "curl",
    "data.table",
    "deldir",
    "digest",
    "dotCall64",
    "dplyr",
    "dqrng",
    "evaluate",
    "farver",
    "fastDummies",
    "fastmap",
    "fitdistrplus",
    "FNN",
    "fontawesome",
    "fs",
    "future",
    "future.apply",
    "generics",
    "ggforce",
    "ggplot2",
    "ggraph",
    "ggrepel",
    "ggridges",
    "globals",
    "glue",
    "goftest",
    "gplots",
    "graphlayouts",
    "gridExtra",
    "gtable",
    "gtools",
    "here",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "ica",
    "igraph",
    "irlba",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "listenv",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "matrixStats",
    "memoise",
    "mime",
    "miniUI",
    "nlme",
    "openssl",
    "otel",
    "parallelly",
    "patchwork",
    "pbapply",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "polyclip",
    "progressr",
    "promises",
    "purrr",
    "R6",
    "RANN",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppHNSW",
    "RcppProgress",
    "RcppTOML",
    "reshape2",
    "reticulate",
    "rlang",
    "rmarkdown",
    "ROCR",
    "rprojroot",
    "RSpectra",
    "Rtsne",
    "S7",
    "sass",
    "scales",
    "scattermore",
    "sctransform",
    "Seurat",
    "SeuratObject",
    "shiny",
    "sitmo",
    "sourcetools",
    "sp",
    "spam",
    "spatstat.data",
    "spatstat.explore",
    "spatstat.geom",
    "spatstat.random",
    "spatstat.sparse",
    "spatstat.univar",
    "spatstat.utils",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "systemfonts",
    "tensor",
    "tibble",
    "tidygraph",
    "tidyr",
    "tidyselect",
    "tinytex",
    "tweenr",
    "utf8",
    "uwot",
    "vctrs",
    "viridis",
    "viridisLite",
    "withr",
    "xfun",
    "xtable",
    "yaml",
    "zoo"
  ],
  "_score": 3.9542425094393248,
  "_indexed": true,
  "_nocasepkg": "scpairs",
  "_universes": [
    "zhaoqing-wang"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.9",
      "date": "2026-07-22T08:17:44.000Z",
      "distro": "resolute",
      "commit": "34ad4a7b3fd3108a7375ac65a27bd335ae7a774f",
      "fileid": "https://r2.ropensci.org/4043b8c243d6f33555855e997b412d7b67c4e9bb1364c4c62522c4ab1a708042",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zhaoqing-wang/actions/runs/29902826427"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.9",
      "date": "2026-07-22T08:17:43.000Z",
      "distro": "resolute",
      "commit": "34ad4a7b3fd3108a7375ac65a27bd335ae7a774f",
      "fileid": "https://r2.ropensci.org/6e5845d8757aff86d9d80172fa364ea746d7d79310f4ae5dfc581bd9c2457ec2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zhaoqing-wang/actions/runs/29902826427"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.9",
      "date": "2026-07-22T08:16:49.000Z",
      "commit": "34ad4a7b3fd3108a7375ac65a27bd335ae7a774f",
      "fileid": "https://r2.ropensci.org/dca0838cb22e0a8bc189a36f5bd16695ef507220e237a5e4c4591e964b3b5dc7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zhaoqing-wang/actions/runs/29902826427"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.9",
      "date": "2026-07-22T08:15:42.000Z",
      "commit": "34ad4a7b3fd3108a7375ac65a27bd335ae7a774f",
      "fileid": "https://r2.ropensci.org/2cadbb989d811eed568a6f6388ab336667bd992280180050ed47f25ea1066092",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zhaoqing-wang/actions/runs/29902826427"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.9",
      "date": "2026-07-22T08:17:49.000Z",
      "commit": "34ad4a7b3fd3108a7375ac65a27bd335ae7a774f",
      "fileid": "https://r2.ropensci.org/e6e38a7b830d7e1b73afa2004b78cd488b1bf464d2c4eb5ed5f450e68d00e230",
      "status": "success",
      "buildurl": "https://github.com/r-universe/zhaoqing-wang/actions/runs/29902826427"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.9",
      "date": "2026-07-22T08:16:02.000Z",
      "commit": "34ad4a7b3fd3108a7375ac65a27bd335ae7a774f",
      "fileid": "https://r2.ropensci.org/c952bcc21dc56f66e58b4773bd5c60df09221f27a82f1fb379e68f020bfe9137",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zhaoqing-wang/actions/runs/29902826427"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.9",
      "date": "2026-07-22T08:15:54.000Z",
      "commit": "34ad4a7b3fd3108a7375ac65a27bd335ae7a774f",
      "fileid": "https://r2.ropensci.org/38cded9ccc3ff4f12df872b71ed5e8ece9f57f23a1eb9e3742f350cdd5cb90e6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zhaoqing-wang/actions/runs/29902826427"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.9",
      "date": "2026-07-22T08:15:53.000Z",
      "commit": "34ad4a7b3fd3108a7375ac65a27bd335ae7a774f",
      "fileid": "https://r2.ropensci.org/d0138ad7a0009316ea051557669451a994f0ddd4e5ddcd2125dc0935303b4b15",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zhaoqing-wang/actions/runs/29902826427"
    }
  ]
}