{
  "_id": "6a19ea8e1d7bb097a09c6c72",
  "Package": "scTenifoldNet",
  "Type": "Package",
  "Title": "Construct and Compare scGRN from Single-Cell Transcriptomic Data",
  "Version": "1.4",
  "Authors@R": "c(person(given = \"Daniel\", family = \"Osorio\", email = \"dcosorioh@utexas.edu\", role = c(\"aut\",\"cre\"), comment = c(ORCID = '0000-0003-4424-8422')),\nperson(given = \"Yan\", family = \"Zhong\", role = c(\"aut\",\"ctb\")),\nperson(given = \"Guanxun\", family = \"Li\", role = c(\"aut\",\"ctb\")),\nperson(given = \"Jianhua\", family = \"Huang\", role = c(\"aut\",\"ctb\")),\nperson(given = \"James\", family = \"Cai\", role = c(\"aut\", \"ctb\", \"ths\"), comment = c(ORCID = '0000-0002-8081-6725'))\n)",
  "Description": "A workflow based on machine learning methods to construct\nand compare single-cell gene regulatory networks (scGRN) using\nsingle-cell RNA-seq (scRNA-seq) data collected from different\nconditions. Uses principal component regression, tensor\ndecomposition, and manifold alignment, to accurately identify\neven subtly shifted gene expression programs. See\n<doi:10.1016/j.patter.2020.100139> for more details.",
  "URL": "https://github.com/cailab-tamu/scTenifoldNet",
  "BugReports": "https://github.com/cailab-tamu/scTenifoldNet/issues",
  "License": "GPL (>=2)",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "Repository": "https://cailab-tamu.r-universe.dev",
  "Date/Publication": "2026-03-26 01:45:45 UTC",
  "RemoteUrl": "https://github.com/cailab-tamu/sctenifoldnet",
  "RemoteRef": "HEAD",
  "RemoteSha": "d7505cf962f7ce8ef4d67b6abf51ea078b59b9c7",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-29 19:29:57 UTC",
    "User": "root"
  },
  "Author": "Daniel Osorio [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-4424-8422>),\nYan Zhong [aut, ctb],\nGuanxun Li [aut, ctb],\nJianhua Huang [aut, ctb],\nJames Cai [aut, ctb, ths] (ORCID:\n<https://orcid.org/0000-0002-8081-6725>)",
  "Maintainer": "Daniel Osorio <dcosorioh@utexas.edu>",
  "MD5sum": "2aff5a72b19bbd22aeba0301f08aed63",
  "_user": "cailab-tamu",
  "_type": "src",
  "_file": "scTenifoldNet_1.4.tar.gz",
  "_fileid": "7ccf07bec972e86d432fad21492fb701aafe3ef68affe1ef391a428f3e45f834",
  "_filesize": 193087,
  "_sha256": "7ccf07bec972e86d432fad21492fb701aafe3ef68affe1ef391a428f3e45f834",
  "_created": "2026-05-29T19:29:57.000Z",
  "_published": "2026-05-29T19:35:42.181Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78572593536,
      "time": 143,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7299366797"
    },
    {
      "job": 78572593575,
      "time": 197,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7299385088"
    },
    {
      "job": 78572593550,
      "time": 137,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7299365282"
    },
    {
      "job": 78572593531,
      "time": 141,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7299366328"
    },
    {
      "job": 78572593568,
      "time": 120,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7299358878"
    },
    {
      "job": 78572593643,
      "time": 226,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7299394427"
    },
    {
      "job": 78572593599,
      "time": 138,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7299365248"
    },
    {
      "job": 78572593557,
      "time": 298,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7299416962"
    },
    {
      "job": 78572079732,
      "time": 191,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7299318955"
    },
    {
      "job": 78572593497,
      "time": 125,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7299360924"
    },
    {
      "job": 78572593538,
      "time": 164,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7299373923"
    },
    {
      "job": 78572593552,
      "time": 182,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7299383078"
    },
    {
      "job": 78572593635,
      "time": 141,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7299366430"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/26657692971",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cailab-tamu/sctenifoldnet",
  "_commit": {
    "id": "d7505cf962f7ce8ef4d67b6abf51ea078b59b9c7",
    "author": "Daniel Osorio <d.osorio@me.com>",
    "committer": "Daniel Osorio <d.osorio@me.com>",
    "message": "Refactor citation format in CITATION file; update documentation for cpDecomposition, cpmNormalization, dRegulation, makeNetworks, manifoldAlignment, pcNet, scQC, and tensorDecomposition functions to improve clarity and consistency. Add C++ backend for pcNet computation with Rcpp integration, including tests for performance validation. Introduce Makevars for package compilation and ensure compatibility across platforms. Update test cases for scQC to reflect changes in expected outputs.\n",
    "time": 1774489545
  },
  "_maintainer": {
    "name": "Daniel Osorio",
    "email": "dcosorioh@utexas.edu",
    "orcid": "0000-0003-4424-8422"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "RSpectra",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "furrr",
      "role": "Imports"
    },
    {
      "package": "future",
      "role": "Imports"
    },
    {
      "package": "RhpcBLASctl",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 2.1.0",
      "role": "Suggests"
    }
  ],
  "_owner": "cailab-tamu",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2026-13",
      "n": 1
    }
  ],
  "_tags": [],
  "_topics": [
    "differential-regulation-analysis",
    "gene-regulatory-networks",
    "manifold-alignment",
    "single-cell",
    "tensor-decomposition",
    "openblas",
    "cpp"
  ],
  "_stars": 37,
  "_contributors": [
    {
      "user": "jamesjcai",
      "count": 140,
      "uuid": 3751222
    },
    {
      "user": "dosorio",
      "count": 51,
      "uuid": 1197740
    },
    {
      "user": "guanxunli",
      "count": 3,
      "uuid": 49222810
    }
  ],
  "_userbio": {
    "uuid": 31963060,
    "type": "organization",
    "name": "Cai Lab at Texas A&M (cailab-tamu)",
    "description": "Single-Cell Biology / Machine Learning / Quantum Computing"
  },
  "_downloads": {
    "count": 2064,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/scTenifoldNet"
  },
  "_devurl": "https://github.com/cailab-tamu/sctenifoldnet",
  "_searchresults": 64,
  "_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/scTenifoldNet.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/cailab-tamu/sctenifoldnet",
  "_realowner": "cailab-tamu",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2019-12-15"
    },
    {
      "version": "1.1.0",
      "date": "2020-01-08"
    },
    {
      "version": "1.2.0",
      "date": "2020-03-10"
    },
    {
      "version": "1.2.1",
      "date": "2020-04-09"
    },
    {
      "version": "1.2.2",
      "date": "2020-05-13"
    },
    {
      "version": "1.2.3",
      "date": "2020-08-26"
    },
    {
      "version": "1.2.4",
      "date": "2020-11-17"
    },
    {
      "version": "1.3",
      "date": "2021-10-29"
    }
  ],
  "_exports": [
    "cpmNormalization",
    "dRegulation",
    "makeNetworks",
    "manifoldAlignment",
    "pcNet",
    "scQC",
    "scTenifoldNet",
    "tensorDecomposition"
  ],
  "_help": [
    {
      "page": "cpDecomposition",
      "title": "Canonical Polyadic Decomposition",
      "topics": [
        "cpDecomposition"
      ]
    },
    {
      "page": "cpmNormalization",
      "title": "Performs counts per million (CPM) data normalization",
      "topics": [
        "cpmNormalization"
      ]
    },
    {
      "page": "dRegulation",
      "title": "Evaluates gene differential regulation based on manifold alignment distances.",
      "topics": [
        "dRegulation"
      ]
    },
    {
      "page": "makeNetworks",
      "title": "Computes gene regulatory networks for subsamples of cells based on principal component regression.",
      "topics": [
        "makeNetworks"
      ]
    },
    {
      "page": "manifoldAlignment",
      "title": "Performs non-linear manifold alignment of two gene regulatory networks.",
      "topics": [
        "manifoldAlignment"
      ]
    },
    {
      "page": "pcNet",
      "title": "Principal Component Network Analysis",
      "topics": [
        "pcNet"
      ]
    },
    {
      "page": "scQC",
      "title": "Performs single-cell data quality control",
      "topics": [
        "scQC"
      ]
    },
    {
      "page": "scTenifoldNet",
      "title": "scTenifoldNet",
      "topics": [
        "scTenifoldNet"
      ]
    },
    {
      "page": "tensorDecomposition",
      "title": "Performs CANDECOMP/PARAFAC (CP) Tensor Decomposition.",
      "topics": [
        "tensorDecomposition"
      ]
    }
  ],
  "_readme": "https://github.com/cailab-tamu/sctenifoldnet/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "codetools",
    "digest",
    "furrr",
    "future",
    "globals",
    "glue",
    "lattice",
    "lifecycle",
    "listenv",
    "magrittr",
    "MASS",
    "Matrix",
    "parallelly",
    "purrr",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RhpcBLASctl",
    "rlang",
    "RSpectra",
    "vctrs"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "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": "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"
    }
  ],
  "_score": 6.4672426413897,
  "_indexed": true,
  "_nocasepkg": "sctenifoldnet",
  "_universes": [
    "cailab-tamu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.4",
      "date": "2026-05-29T19:32:07.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "d7505cf962f7ce8ef4d67b6abf51ea078b59b9c7",
      "fileid": "f8d9ad97fa4b12d41b62eb69132b2750ead3bc104cfab6d3f20b5785e54e51e8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/26657692971"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.4",
      "date": "2026-05-29T19:32:54.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "d7505cf962f7ce8ef4d67b6abf51ea078b59b9c7",
      "fileid": "6d30f4438edb0266976c2c734d7473472f157013716f30f9200e76375d4cdacd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/26657692971"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.4",
      "date": "2026-05-29T19:32:02.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "d7505cf962f7ce8ef4d67b6abf51ea078b59b9c7",
      "fileid": "f9c337371de5afa942d19588526b951b00dfd71f3164aa5736739a77416b77d1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/26657692971"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.4",
      "date": "2026-05-29T19:31:57.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "d7505cf962f7ce8ef4d67b6abf51ea078b59b9c7",
      "fileid": "329b152805ad66f080a2f2e62ec6b9bde676331b5645d401d1158889a63b436b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/26657692971"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.4",
      "date": "2026-05-29T19:31:38.000Z",
      "arch": "aarch64",
      "commit": "d7505cf962f7ce8ef4d67b6abf51ea078b59b9c7",
      "fileid": "9178e9e919c49f6fadfaa74e62fbc2da723ab0e166bec77694fd3bdae73d8b6d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/26657692971"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.4",
      "date": "2026-05-29T19:32:58.000Z",
      "arch": "x86_64",
      "commit": "d7505cf962f7ce8ef4d67b6abf51ea078b59b9c7",
      "fileid": "5a5fcdd82d7705b16f8ae19b61ffe6771fd9c41f0a6a30bd6de426b4665b2bf4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/26657692971"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.4",
      "date": "2026-05-29T19:31:41.000Z",
      "arch": "aarch64",
      "commit": "d7505cf962f7ce8ef4d67b6abf51ea078b59b9c7",
      "fileid": "b846611f0834de4ae63a82849a4743ba1bf9f79d3cbc5689c204c1248788df1c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/26657692971"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.4",
      "date": "2026-05-29T19:33:22.000Z",
      "arch": "x86_64",
      "commit": "d7505cf962f7ce8ef4d67b6abf51ea078b59b9c7",
      "fileid": "cffff398748c196ef11a5a66e33bb3adbb45ca40fb412f8941f20fde2ca2ec5e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/26657692971"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.4",
      "date": "2026-05-29T19:32:22.000Z",
      "arch": "emscripten",
      "commit": "d7505cf962f7ce8ef4d67b6abf51ea078b59b9c7",
      "fileid": "35e4630313e9ea226be6744bd7afda1eb145d458ed511d2984abeb91619f27a5",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/26657692971"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.4",
      "date": "2026-05-29T19:31:32.000Z",
      "arch": "x86_64",
      "commit": "d7505cf962f7ce8ef4d67b6abf51ea078b59b9c7",
      "fileid": "5ba9a7809e31e30ce236fb6e67ac21b8334c8622f7db528111ae03e966f7e1f4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/26657692971"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.4",
      "date": "2026-05-29T19:31:57.000Z",
      "arch": "x86_64",
      "commit": "d7505cf962f7ce8ef4d67b6abf51ea078b59b9c7",
      "fileid": "0f03e07cd422178d0a7e55506f8d8a5a512daa7a60808b3b5b484a545d5a3500",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/26657692971"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.4",
      "date": "2026-05-29T19:31:23.000Z",
      "arch": "x86_64",
      "commit": "d7505cf962f7ce8ef4d67b6abf51ea078b59b9c7",
      "fileid": "3ffa0bb59e95d4c704ddf158b39293cfcfd5e3bd26a3f0420ca610a439a28d64",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/26657692971"
    }
  ]
}