{
  "_id": "6a197913acfb0bcc41df4157",
  "Package": "SCORPION",
  "Type": "Package",
  "Title": "Single Cell Oriented Reconstruction of PANDA Individual\nOptimized Networks",
  "Version": "1.2.2",
  "Authors@R": "c(\nperson(\"Zaoqu\", \"Liu\", email = \"liuzaoqu@163.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0452-742X\")),\nperson(\"Daniel\", \"Osorio\", email = \"daniecos@uio.no\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-4424-8422\")),\nperson(\"Marieke L.\", \"Kuijjer\", email = \"marieke.kuijjer@ncmm.uio.no\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-6280-3130\")))",
  "Description": "Constructs gene regulatory networks from single-cell gene\nexpression data using the PANDA (Passing Attributes between\nNetworks for Data Assimilation) algorithm.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "URL": "https://zaoqu-liu.github.io/SCORPION/,\nhttps://github.com/Zaoqu-Liu/SCORPION",
  "BugReports": "https://github.com/Zaoqu-Liu/SCORPION/issues",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://zaoqu-liu.r-universe.dev",
  "Date/Publication": "2026-01-29 07:46:57 UTC",
  "RemoteUrl": "https://github.com/Zaoqu-Liu/SCORPION",
  "RemoteRef": "main",
  "RemoteSha": "c01e59eb2edec1b16a9723eeb1c4b08c8c3f4b7b",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-29 09:56:57 UTC",
    "User": "root"
  },
  "Author": "Zaoqu Liu [aut, cre] (ORCID: <https://orcid.org/0000-0002-0452-742X>),\nDaniel Osorio [aut] (ORCID: <https://orcid.org/0000-0003-4424-8422>),\nMarieke L. Kuijjer [aut] (ORCID:\n<https://orcid.org/0000-0001-6280-3130>)",
  "Maintainer": "Zaoqu Liu <liuzaoqu@163.com>",
  "MD5sum": "f17754a2549e9044f234ca65a6488070",
  "_user": "zaoqu-liu",
  "_type": "src",
  "_file": "SCORPION_1.2.2.tar.gz",
  "_fileid": "282deedaa52b0cb9909206f88585a1f18d6b4fa1fc805260856eb9478c8746cd",
  "_filesize": 3154588,
  "_sha256": "282deedaa52b0cb9909206f88585a1f18d6b4fa1fc805260856eb9478c8746cd",
  "_created": "2026-05-29T09:56:57.000Z",
  "_published": "2026-05-29T11:31:31.963Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78478886402,
      "time": 187,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7288088939"
    },
    {
      "job": 78478886381,
      "time": 198,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7288092269"
    },
    {
      "job": 78478886389,
      "time": 183,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288087920"
    },
    {
      "job": 78478886413,
      "time": 205,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288094442"
    },
    {
      "job": 78478886388,
      "time": 224,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7289636040"
    },
    {
      "job": 78478886403,
      "time": 506,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7288183189"
    },
    {
      "job": 78478886374,
      "time": 203,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7289638515"
    },
    {
      "job": 78478886354,
      "time": 299,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288152134"
    },
    {
      "job": 78478049499,
      "time": 333,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288033310"
    },
    {
      "job": 78478886325,
      "time": 177,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288085733"
    },
    {
      "job": 78478886411,
      "time": 542,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7288192660"
    },
    {
      "job": 78478886350,
      "time": 540,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7288192205"
    },
    {
      "job": 78478886377,
      "time": 521,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288186440"
    }
  ],
  "_buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26630550773",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/Zaoqu-Liu/SCORPION",
  "_commit": {
    "id": "c01e59eb2edec1b16a9723eeb1c4b08c8c3f4b7b",
    "author": "Zaoqu-Liu <liuzaoqu@163.com>",
    "committer": "Zaoqu-Liu <liuzaoqu@163.com>",
    "message": "Fix code review issues\n\n- Add missing igraph::E import to buildKNND.R\n- Simplify normalizeNetwork.R for robustness with dense matrix operations\n- Fix pcNet.R Windows cluster to use requireNamespace instead of library\n- Remove C++11 specification from Makevars (not required)\n",
    "time": 1769672817
  },
  "_maintainer": {
    "name": "Zaoqu Liu",
    "email": "liuzaoqu@163.com",
    "login": "zaoqu-liu",
    "orcid": "0000-0002-0452-742X",
    "description": "AI4S",
    "uuid": 68080738
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "irlba",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "RANN",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "pbapply",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "RhpcBLASctl",
      "role": "Suggests"
    },
    {
      "package": "gpuR",
      "role": "Suggests"
    },
    {
      "package": "matrixStats",
      "role": "Suggests"
    },
    {
      "package": "Seurat",
      "role": "Suggests"
    },
    {
      "package": "SeuratObject",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "zaoqu-liu",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-05",
      "n": 10
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "zaoqu-liu",
      "count": 10,
      "uuid": 68080738
    }
  ],
  "_userbio": {
    "uuid": 68080738,
    "type": "user",
    "name": "LIU Zaoqu",
    "description": "AI4S"
  },
  "_downloads": {
    "count": 557,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SCORPION"
  },
  "_devurl": "https://github.com/zaoqu-liu/scorpion",
  "_pkgdown": "https://zaoqu-liu.github.io/SCORPION/",
  "_searchresults": 21,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/SCORPION.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/kuijjerlab/scorpion",
  "_realowner": "kuijjerlab",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2022-09-21"
    },
    {
      "version": "1.0.1",
      "date": "2022-09-22"
    },
    {
      "version": "1.0.2",
      "date": "2024-05-29"
    },
    {
      "version": "1.1.0",
      "date": "2025-08-25"
    },
    {
      "version": "1.2.0",
      "date": "2025-09-24"
    },
    {
      "version": "1.3.0",
      "date": "2026-02-04"
    },
    {
      "version": "1.3.1",
      "date": "2026-02-16"
    },
    {
      "version": "1.3.2",
      "date": "2026-03-10"
    }
  ],
  "_exports": [
    "scorpion"
  ],
  "_datasets": [
    {
      "name": "scorpionTest",
      "title": "Example single-cell gene expression, motif, and ppi data",
      "object": "scorpionTest",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "scorpion",
      "title": "Constructs PANDA gene regulatory networks from single-cell gene expression data",
      "topics": [
        "scorpion"
      ]
    },
    {
      "page": "scorpionTest",
      "title": "Example single-cell gene expression, motif, and ppi data",
      "topics": [
        "scorpionTest"
      ]
    }
  ],
  "_readme": "https://github.com/Zaoqu-Liu/SCORPION/raw/main/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "glue",
    "igraph",
    "irlba",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "pbapply",
    "pkgconfig",
    "RANN",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "vctrs"
  ],
  "_sysdeps": [
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "advanced-usage.Rmd",
      "filename": "advanced-usage.html",
      "title": "Advanced Usage and Best Practices",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Parameter Tuning",
        "Gamma Value (Metacell Aggregation)",
        "Alpha Value (Learning Rate)",
        "Hamming Threshold",
        "Association Methods",
        "Pearson Correlation (Default)",
        "Spearman Correlation",
        "Principal Component Regression (pcNet)",
        "Comparison",
        "Working with Seurat Objects",
        "Filtering and Preprocessing",
        "Filter Low-Expression Genes",
        "Custom Gene Filtering",
        "Parallel Processing",
        "Output Analysis",
        "Network Comparison",
        "Differential Network Analysis",
        "Best Practices",
        "1. Data Quality",
        "2. Prior Network Selection",
        "3. Parameter Selection",
        "4. Reproducibility",
        "Session Information"
      ],
      "created": "2026-01-29 07:08:39",
      "modified": "2026-01-29 07:08:39",
      "commits": 1
    },
    {
      "source": "algorithm.Rmd",
      "filename": "algorithm.html",
      "title": "Algorithm and Mathematical Framework",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "The PANDA Algorithm",
        "Core Concept",
        "Mathematical Formulation",
        "1. Tanimoto Similarity",
        "2. Network Update Rules",
        "Convergence Criterion",
        "Metacell Aggregation",
        "The Sparsity Problem",
        "Solution: Metacells",
        "Gamma Parameter",
        "Network Normalization",
        "Double Z-score Normalization",
        "Computational Complexity",
        "References",
        "Session Information"
      ],
      "created": "2026-01-29 07:08:39",
      "modified": "2026-01-29 07:08:39",
      "commits": 1
    },
    {
      "source": "network-visualization.Rmd",
      "filename": "network-visualization.html",
      "title": "Network Visualization",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Running SCORPION",
        "Network Statistics Visualization",
        "Edge Weight Distribution",
        "TF Targeting Statistics",
        "Heatmap Visualization",
        "Regulatory Network Heatmap",
        "TF Cooperation Heatmap",
        "Network Graph Visualization",
        "Building igraph Network",
        "Network Layout and Plotting",
        "Subnetwork for Specific TF",
        "Circular Network Plot",
        "Network Centrality Analysis",
        "Exporting Networks",
        "Export to Cytoscape",
        "Export to GraphML",
        "Summary",
        "Session Information"
      ],
      "created": "2026-01-29 07:08:39",
      "modified": "2026-01-29 07:08:39",
      "commits": 1
    },
    {
      "source": "quick-start.Rmd",
      "filename": "quick-start.html",
      "title": "Quick Start Guide",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Loading the Package",
        "Example Data",
        "Running SCORPION",
        "Output Structure",
        "Extracting Top Regulatory Edges",
        "Visualizing Network Statistics",
        "Session Information"
      ],
      "created": "2026-01-29 07:08:39",
      "modified": "2026-01-29 07:08:39",
      "commits": 1
    }
  ],
  "_score": 3.623249290397901,
  "_indexed": false,
  "_nocasepkg": "scorpion",
  "_universes": [
    "zaoqu-liu"
  ],
  "_indexurl": "https://kuijjerlab.r-universe.dev/SCORPION",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.2",
      "date": "2026-05-29T09:59:55.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "c01e59eb2edec1b16a9723eeb1c4b08c8c3f4b7b",
      "fileid": "3f2ca53951224bbac684da7a66f6503894705626139c00e8fe94097060f57575",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26630550773"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.2",
      "date": "2026-05-29T10:00:02.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "c01e59eb2edec1b16a9723eeb1c4b08c8c3f4b7b",
      "fileid": "e063732c23e7ff4cf3f99fbd4cf75a648f357d5aeb41c7db3071fad0c74bf8a2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26630550773"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2.2",
      "date": "2026-05-29T09:59:54.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "c01e59eb2edec1b16a9723eeb1c4b08c8c3f4b7b",
      "fileid": "f3cf106aa03f4573f18b6826e986732596c1189bdc5de8a88d39eda7d128f32f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26630550773"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2.2",
      "date": "2026-05-29T10:00:08.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "c01e59eb2edec1b16a9723eeb1c4b08c8c3f4b7b",
      "fileid": "5942f4942e257596983da03fac6af89907fc444b89ac4e69fe9c74b68f0d784d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26630550773"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.2",
      "date": "2026-05-29T11:30:29.000Z",
      "arch": "aarch64",
      "commit": "c01e59eb2edec1b16a9723eeb1c4b08c8c3f4b7b",
      "fileid": "118a281424650a2fc6c25e2e71269de2919d850f358372efe11bb9f0dc91e15d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26630550773"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.2",
      "date": "2026-05-29T10:04:58.000Z",
      "arch": "x86_64",
      "commit": "c01e59eb2edec1b16a9723eeb1c4b08c8c3f4b7b",
      "fileid": "7cc44a4546f41652ff758abbd569db85fc164ee004933e187d2570eba96b054e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26630550773"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.2.2",
      "date": "2026-05-29T11:30:44.000Z",
      "arch": "aarch64",
      "commit": "c01e59eb2edec1b16a9723eeb1c4b08c8c3f4b7b",
      "fileid": "aff69c8837d3a69a5d248adcdc0718b204f17f326c6e6485b242ec66fc83f357",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26630550773"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.2.2",
      "date": "2026-05-29T10:02:43.000Z",
      "arch": "x86_64",
      "commit": "c01e59eb2edec1b16a9723eeb1c4b08c8c3f4b7b",
      "fileid": "3673ffe7c3d3fd6858ae8e4892fb6ba5f310ac3cd4d85e6e048e54fc0f04ed1c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26630550773"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2.2",
      "date": "2026-05-29T10:00:12.000Z",
      "arch": "emscripten",
      "commit": "c01e59eb2edec1b16a9723eeb1c4b08c8c3f4b7b",
      "fileid": "6d406fda5745964707ac44f5206e9493131226653355d603b0dccc511316ab4a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26630550773"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2.2",
      "date": "2026-05-29T10:04:37.000Z",
      "arch": "x86_64",
      "commit": "c01e59eb2edec1b16a9723eeb1c4b08c8c3f4b7b",
      "fileid": "bfa3936636ccf06f9fef737cf839550e79be8aa3ce3ddce87d57fd08200355c9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26630550773"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2.2",
      "date": "2026-05-29T10:05:27.000Z",
      "arch": "x86_64",
      "commit": "c01e59eb2edec1b16a9723eeb1c4b08c8c3f4b7b",
      "fileid": "119619fb5ac94dae5b9a331d0e7232d463d92ed3309367e1f58ccf761806afbd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26630550773"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.2.2",
      "date": "2026-05-29T10:04:48.000Z",
      "arch": "x86_64",
      "commit": "c01e59eb2edec1b16a9723eeb1c4b08c8c3f4b7b",
      "fileid": "c611671a6024cd984262ee1d422654e75a040310e787c9ab4fb06f4f78c22450",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26630550773"
    }
  ]
}