{
  "_id": "6a5359f79b92047c28d58562",
  "Package": "markerpen",
  "Type": "Package",
  "Title": "Marker Gene Detection via Penalized Principal Component Analysis",
  "Version": "0.1.2",
  "Date": "2025-12-14",
  "Authors@R": "c(\nperson(\"Yixuan\", \"Qiu\",\nemail = \"yixuan.qiu@cos.name\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Jiebiao\", \"Wang\", role = \"aut\"),\nperson(\"Jing\", \"Lei\", role = \"aut\"),\nperson(\"Kathryn\", \"Roeder\", role = \"aut\"))",
  "Description": "Implementation of the 'MarkerPen' algorithm, short for\nmarker gene detection via penalized principal component\nanalysis, described in the paper by Qiu, Wang, Lei, and Roeder\n(2021, <doi:10.1093/bioinformatics/btab257>). 'MarkerPen' is a\nsemi-supervised algorithm for detecting marker genes by\ncombining prior marker information with bulk transcriptome\ndata.",
  "License": "GPL",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "VignetteBuilder": "knitr, rmarkdown",
  "RoxygenNote": "7.3.2",
  "Repository": "https://yixuan.r-universe.dev",
  "Date/Publication": "2025-12-14 12:33:32 UTC",
  "RemoteUrl": "https://github.com/yixuan/markerpen",
  "RemoteRef": "HEAD",
  "RemoteSha": "b521abf5ef3ff9d9cc23253559d45ed6478c1979",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-12 09:04:28 UTC",
    "User": "root"
  },
  "Author": "Yixuan Qiu [aut, cre],\nJiebiao Wang [aut],\nJing Lei [aut],\nKathryn Roeder [aut]",
  "Maintainer": "Yixuan Qiu <yixuan.qiu@cos.name>",
  "_user": "yixuan",
  "_type": "src",
  "_file": "markerpen_0.1.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/73ade7a16df5277c307c2fd574c374699e450aa0f0011fa6bb07da9dddbe434c",
  "_filesize": 4310034,
  "_sha256": "73ade7a16df5277c307c2fd574c374699e450aa0f0011fa6bb07da9dddbe434c",
  "_expires": "2026-10-20T09:10:13.000Z",
  "_created": "2026-07-12T09:04:28.000Z",
  "_published": "2026-07-12T09:10:15.559Z",
  "_jobs": [
    {
      "job": 86634536352,
      "time": 183,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8258311261"
    },
    {
      "job": 86634536445,
      "time": 178,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8258310370"
    },
    {
      "job": 86634536391,
      "time": 152,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8258307303"
    },
    {
      "job": 86634536372,
      "time": 182,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8258310824"
    },
    {
      "job": 86634536369,
      "time": 108,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8258301245"
    },
    {
      "job": 86634536357,
      "time": 240,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8258318082"
    },
    {
      "job": 86634536379,
      "time": 110,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8258301528"
    },
    {
      "job": 86634536378,
      "time": 285,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8258323811"
    },
    {
      "job": 86634246639,
      "time": 225,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8258286512"
    },
    {
      "job": 86634536309,
      "time": 121,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 86634536332,
      "time": 136,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8258304611"
    },
    {
      "job": 86634536370,
      "time": 148,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8258306199"
    },
    {
      "job": 86634536333,
      "time": 141,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8258305327"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/yixuan/actions/runs/29186769120",
  "_status": "success",
  "_upstream": "https://github.com/yixuan/markerpen",
  "_commit": {
    "id": "b521abf5ef3ff9d9cc23253559d45ed6478c1979",
    "author": "Yixuan Qiu <yixuanq@gmail.com>",
    "committer": "Yixuan Qiu <yixuanq@gmail.com>",
    "message": "remove CXX_STD\n",
    "time": 1765715612
  },
  "_maintainer": {
    "name": "Yixuan Qiu",
    "email": "yixuan.qiu@cos.name",
    "login": "yixuan",
    "description": "",
    "uuid": 216398
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "RSpectra",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.1",
      "role": "Imports"
    },
    {
      "package": "RSpectra",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "prettydoc",
      "role": "Suggests"
    },
    {
      "package": "scales",
      "role": "Suggests"
    }
  ],
  "_owner": "yixuan",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-50",
      "n": 7
    }
  ],
  "_tags": [],
  "_stars": 6,
  "_contributors": [
    {
      "user": "yixuan",
      "count": 71,
      "uuid": 216398
    }
  ],
  "_userbio": {
    "uuid": 216398,
    "type": "user",
    "name": "Yixuan Qiu",
    "followers": 904
  },
  "_downloads": {
    "count": 329,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/markerpen"
  },
  "_devurl": "https://github.com/yixuan/markerpen",
  "_searchresults": 4,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/markerpen.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/yixuan/markerpen",
  "_realowner": "yixuan",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2021-03-11"
    },
    {
      "version": "0.1.1",
      "date": "2021-03-17"
    },
    {
      "version": "0.1.2",
      "date": "2025-12-14"
    }
  ],
  "_exports": [
    "pca_pen",
    "refine_markers",
    "sort_markers"
  ],
  "_datasets": [
    {
      "name": "gene_mapping",
      "title": "Mapping gene names to Ensembl IDs",
      "object": "gene_mapping",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ensembl",
        "name"
      ],
      "rows": 59074,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "gene_mapping",
      "title": "Mapping gene names to Ensembl IDs",
      "topics": [
        "gene_mapping"
      ]
    },
    {
      "page": "pca_pen",
      "title": "Penalized Principal Component Analysis for Marker Gene Selection",
      "topics": [
        "pca_pen"
      ]
    },
    {
      "page": "refine_markers",
      "title": "Marker Gene Selection via Penalized Principal Component Analysis",
      "topics": [
        "refine_markers"
      ]
    },
    {
      "page": "sort_markers",
      "title": "Post-processing Selected Marker Genes",
      "topics": [
        "sort_markers"
      ]
    }
  ],
  "_readme": "https://github.com/yixuan/markerpen/raw/HEAD/README.md",
  "_rundeps": [
    "lattice",
    "Matrix",
    "Rcpp",
    "RcppEigen",
    "RSpectra"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "introduction.Rmd",
      "filename": "introduction.html",
      "title": "MarkerPen: Marker Gene Detection via Penalized Principal Component Analysis",
      "author": "Yixuan Qiu, Jiebiao Wang, Jing Lei, and Kathryn Roeder",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Example"
      ],
      "created": "2021-02-28 10:00:21",
      "modified": "2025-12-14 12:02:45",
      "commits": 4
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": true,
  "_nocasepkg": "markerpen",
  "_universes": [
    "yixuan"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-07-12T09:07:28.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "b521abf5ef3ff9d9cc23253559d45ed6478c1979",
      "fileid": "https://r2.ropensci.org/0be0f7157ee241adfdd33c8ed44582e3d4a85a5db8294c57aa4fd4175a7ad242",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yixuan/actions/runs/29186769120"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-07-12T09:07:10.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "b521abf5ef3ff9d9cc23253559d45ed6478c1979",
      "fileid": "https://r2.ropensci.org/bb3994bd3ff4f0442d7b458888fe3cc7f09c0de96f21ecae8c378e99e440247c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yixuan/actions/runs/29186769120"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-07-12T09:07:00.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "b521abf5ef3ff9d9cc23253559d45ed6478c1979",
      "fileid": "https://r2.ropensci.org/dcefde46d16fb4bb4240cb975418a6cec7d50fa81f9cc6722c0b9f1c421d9cc7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yixuan/actions/runs/29186769120"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-07-12T09:07:14.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "b521abf5ef3ff9d9cc23253559d45ed6478c1979",
      "fileid": "https://r2.ropensci.org/2e01fc5dd2c3db6f8f7c69c9bf6b01e86d239e196ba27f917458af0e26a416ad",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yixuan/actions/runs/29186769120"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-07-12T09:06:16.000Z",
      "arch": "aarch64",
      "commit": "b521abf5ef3ff9d9cc23253559d45ed6478c1979",
      "fileid": "https://r2.ropensci.org/3652c7abf4420ea6b0929d8979a97bb2e1faf7154ad1a154f8ae4e21ea43c3bb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yixuan/actions/runs/29186769120"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-07-12T09:07:47.000Z",
      "arch": "x86_64",
      "commit": "b521abf5ef3ff9d9cc23253559d45ed6478c1979",
      "fileid": "https://r2.ropensci.org/383a0fe94a095d781b7772f0e4b163f10b35cd8e6d41b5194ba38fb34baf1095",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yixuan/actions/runs/29186769120"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-07-12T09:06:19.000Z",
      "arch": "aarch64",
      "commit": "b521abf5ef3ff9d9cc23253559d45ed6478c1979",
      "fileid": "https://r2.ropensci.org/f90ae33da422d4bf0cffe8e7d9c4272dddc110ac2e88ea7aafffc06c250e2dd1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yixuan/actions/runs/29186769120"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-07-12T09:08:10.000Z",
      "arch": "x86_64",
      "commit": "b521abf5ef3ff9d9cc23253559d45ed6478c1979",
      "fileid": "https://r2.ropensci.org/40329cfba754e6fedc51db16d5652de4c084369dfad464ee9e726e7df21442b1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yixuan/actions/runs/29186769120"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-07-12T09:05:57.000Z",
      "arch": "x86_64",
      "commit": "b521abf5ef3ff9d9cc23253559d45ed6478c1979",
      "fileid": "https://r2.ropensci.org/0d276440377768994b029659b18915d2e22e7c9eb67a097a7cc63165e1be1ac5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yixuan/actions/runs/29186769120"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-07-12T09:05:59.000Z",
      "arch": "x86_64",
      "commit": "b521abf5ef3ff9d9cc23253559d45ed6478c1979",
      "fileid": "https://r2.ropensci.org/9bf011bff31fc76fb859f3dadfc3f2ce5609f8698c1c29d6bcdac6fcd53dc142",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yixuan/actions/runs/29186769120"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-07-12T09:06:04.000Z",
      "arch": "x86_64",
      "commit": "b521abf5ef3ff9d9cc23253559d45ed6478c1979",
      "fileid": "https://r2.ropensci.org/01a0d3ba608dd06e181467752708286ae7b8d4e554ad166cf4e68088c92fe57f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yixuan/actions/runs/29186769120"
    }
  ]
}