{
  "_id": "6a49f0a49a8f074f7420544e",
  "Package": "SMDIC",
  "Type": "Package",
  "Title": "Identification of Somatic Mutation-Driven Immune Cells",
  "Version": "0.1.6",
  "Authors@R": "c(\nperson(\"Junwei\", \"Han\", email = \"hanjunwei1981@163.com\", role = \"cre\"),\nperson(\"Baotong\", \"Zheng\", email = \"btzheng1116@163.com\", role = \"aut\"))",
  "Maintainer": "Junwei Han <hanjunwei1981@163.com>",
  "Description": "A computing tool is developed to automated identify\nsomatic mutation-driven immune cells. The operation modes\nincluding: i) inferring the relative abundance matrix of\ntumor-infiltrating immune cells and integrating it with a\nparticular gene mutation status, ii) detecting differential\nimmune cells with respect to the gene mutation status and\nconverting the abundance matrix of significant differential\nimmune cell into two binary matrices (one for up-regulated and\none for down-regulated), iii) identifying somatic\nmutation-driven immune cells by comparing the gene mutation\nstatus with each immune cell in the binary matrices across all\nsamples, and iv) visualization of immune cell abundance of\nsamples in different mutation status..",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.2",
  "biocViews": "",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake make libmagick++-dev gsfonts libbz2-dev\nlibicu-dev libjpeg-dev liblzma-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://hanjunwei-lab.r-universe.dev",
  "Date/Publication": "2024-10-17 01:15:49 UTC",
  "RemoteUrl": "https://github.com/hanjunwei-lab/smdic",
  "RemoteRef": "HEAD",
  "RemoteSha": "70ba7d1dc794c4a4cf862cb7f0d0f75130d68c67",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-13 08:43:03 UTC",
    "User": "root"
  },
  "Author": "Junwei Han [cre],\nBaotong Zheng [aut]",
  "_user": "hanjunwei-lab",
  "_type": "src",
  "_file": "SMDIC_0.1.6.tar.gz",
  "_fileid": "https://r2.ropensci.org/20da310e7477632cf646b1678e1772441813220e4c51d164287009c1b6fc4661",
  "_filesize": 3688533,
  "_sha256": "20da310e7477632cf646b1678e1772441813220e4c51d164287009c1b6fc4661",
  "_expires": "2026-10-13T05:50:26.000Z",
  "_created": "2026-06-13T08:43:03.000Z",
  "_published": "2026-07-05T05:50:28.297Z",
  "_jobs": [
    {
      "job": 85196852162,
      "time": 416,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7609245698"
    },
    {
      "job": 85196852243,
      "time": 409,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7609244901"
    },
    {
      "job": 85196852207,
      "time": 201,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7609220847"
    },
    {
      "job": 85196852282,
      "time": 262,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7609227780"
    },
    {
      "job": 85196852117,
      "time": 322,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7609198297"
    },
    {
      "job": 85196852238,
      "time": 192,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7609220497"
    },
    {
      "job": 85196852216,
      "time": 294,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7609231436"
    },
    {
      "job": 85196852240,
      "time": 332,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7609235817"
    },
    {
      "job": 85196852242,
      "time": 309,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7609233077"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/27461858756",
  "_status": "success",
  "_upstream": "https://github.com/hanjunwei-lab/smdic",
  "_commit": {
    "id": "70ba7d1dc794c4a4cf862cb7f0d0f75130d68c67",
    "author": "hanjunwei-lab <hanjunwei1981@163.com>",
    "committer": "hanjunwei-lab <hanjunwei1981@163.com>",
    "message": "update 0.1.6 version\n",
    "time": 1729127749
  },
  "_maintainer": {
    "name": "Junwei Han",
    "email": "hanjunwei1981@163.com",
    "login": "hanjunwei-lab",
    "description": "Junwei Han is a professor in Harbin Medical University. His research is in the areas of bioinformatics and computational systems biology.",
    "uuid": 60877533
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "GSVA",
      "role": "Depends"
    },
    {
      "package": "samr",
      "role": "Imports"
    },
    {
      "package": "e1071",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "preprocessCore",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "maftools",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "survival",
      "role": "Imports"
    },
    {
      "package": "survminer",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "pracma",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "backports",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "R.utils",
      "role": "Suggests"
    }
  ],
  "_owner": "hanjunwei-lab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 2,
  "_contributors": [
    {
      "user": "hanjunwei-lab",
      "count": 39,
      "uuid": 60877533
    }
  ],
  "_userbio": {
    "uuid": 60877533,
    "type": "user",
    "name": "Junwei Han",
    "description": "Junwei Han is a professor in Harbin Medical University. His research is in the areas of bioinformatics and computational systems biology."
  },
  "_downloads": {
    "count": 315,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SMDIC"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/hanjunwei-lab/smdic",
  "_searchresults": 6,
  "_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/SMDIC.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/hanjunwei-lab/smdic",
  "_realowner": "hanjunwei-lab",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2020-06-16"
    },
    {
      "version": "0.1.1",
      "date": "2020-06-21"
    },
    {
      "version": "0.1.2",
      "date": "2020-07-05"
    },
    {
      "version": "0.1.3",
      "date": "2020-11-13"
    },
    {
      "version": "0.1.4",
      "date": "2023-08-29"
    },
    {
      "version": "0.1.5",
      "date": "2024-01-12"
    },
    {
      "version": "0.1.6",
      "date": "2024-10-16"
    }
  ],
  "_exports": [
    "exp2cell",
    "gene2cellsummary",
    "GetExampleData",
    "heatmapcell",
    "maf2matrix",
    "mutcellsummary",
    "mutcorcell",
    "plotCoocMutex",
    "plotwaterfall",
    "survcell"
  ],
  "_datasets": [
    {
      "name": "envData",
      "title": "envData",
      "object": "envData",
      "class": [
        "environment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "xCell.data",
      "title": "xCell datasets",
      "object": "xCell.data",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "SMDIC-package",
      "title": "Identification of somatic mutation-driven immune cells",
      "topics": [
        "SMDIC-package",
        "SMDIC"
      ]
    },
    {
      "page": "cell24",
      "title": "A data.frame of 24 immune cells name from Bindea et al",
      "topics": [
        "cell24"
      ]
    },
    {
      "page": "cell64",
      "title": "A data.frame of 64 immune cells name from xCell method",
      "topics": [
        "cell64"
      ]
    },
    {
      "page": "envData",
      "title": "envData",
      "topics": [
        "cellmatrix",
        "envData",
        "exp.example",
        "mutcell",
        "mutmatrix"
      ]
    },
    {
      "page": "exp2cell",
      "title": "exp2cell",
      "topics": [
        "exp2cell"
      ]
    },
    {
      "page": "gene2cellsummary",
      "title": "gene2cellsummary",
      "topics": [
        "gene2cellsummary"
      ]
    },
    {
      "page": "GetExampleData",
      "title": "Get the example data",
      "topics": [
        "GetExampleData"
      ]
    },
    {
      "page": "heatmapcell",
      "title": "heatmapcell",
      "topics": [
        "heatmapcell"
      ]
    },
    {
      "page": "immunelist",
      "title": "A large list of 24 immune cells type-specific gene signatures from Bindea et al",
      "topics": [
        "immunelist"
      ]
    },
    {
      "page": "maf2matrix",
      "title": "maf2matrix",
      "topics": [
        "maf2matrix"
      ]
    },
    {
      "page": "mutcellsummary",
      "title": "mutcellsummary",
      "topics": [
        "mutcellsummary"
      ]
    },
    {
      "page": "mutcorcell",
      "title": "mutcorcell",
      "topics": [
        "mutcorcell"
      ]
    },
    {
      "page": "plotCoocMutex",
      "title": "plotCoocMutex",
      "topics": [
        "plotCoocMutex"
      ]
    },
    {
      "page": "plotwaterfall",
      "title": "plotwaterfall",
      "topics": [
        "plotwaterfall"
      ]
    },
    {
      "page": "survcell",
      "title": "survcell",
      "topics": [
        "survcell"
      ]
    },
    {
      "page": "xCell.data",
      "title": "xCell datasets",
      "topics": [
        "xCell.data"
      ]
    }
  ],
  "_readme": "https://github.com/hanjunwei-lab/smdic/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "assorthead",
    "backports",
    "base64enc",
    "beachmat",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "biocmake",
    "BiocParallel",
    "BiocSingular",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "boot",
    "broom",
    "bslib",
    "cachem",
    "car",
    "carData",
    "class",
    "cli",
    "codetools",
    "colorspace",
    "commonmark",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "DelayedMatrixStats",
    "Deriv",
    "digest",
    "dir.expiry",
    "DNAcopy",
    "doBy",
    "dplyr",
    "e1071",
    "exactRankTests",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "forecast",
    "formatR",
    "Formula",
    "fracdiff",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "ggtext",
    "glue",
    "graph",
    "gridExtra",
    "gridtext",
    "GSA",
    "GSEABase",
    "GSVA",
    "gtable",
    "h5mread",
    "HDF5Array",
    "htmltools",
    "httpuv",
    "httr",
    "httr2",
    "impute",
    "IRanges",
    "irlba",
    "isoband",
    "jpeg",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lifecycle",
    "litedown",
    "lme4",
    "lmtest",
    "maftools",
    "magick",
    "magrittr",
    "markdown",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "maxstat",
    "memoise",
    "memuse",
    "mgcv",
    "microbenchmark",
    "mime",
    "minqa",
    "modelr",
    "mvtnorm",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "openssl",
    "openxlsx",
    "otel",
    "pbkrtest",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "png",
    "polynom",
    "pracma",
    "preprocessCore",
    "promises",
    "proxy",
    "purrr",
    "quantreg",
    "R6",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "Rhtslib",
    "rjson",
    "rlang",
    "RSQLite",
    "rstatix",
    "rsvd",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "samr",
    "sass",
    "ScaledMatrix",
    "scales",
    "Seqinfo",
    "shiny",
    "shinyFiles",
    "SingleCellExperiment",
    "snow",
    "sourcetools",
    "SparseArray",
    "SparseM",
    "sparseMatrixStats",
    "SpatialExperiment",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "survminer",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "zip",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "SMDIC.Rmd",
      "filename": "SMDIC.html",
      "title": "SMDIC User Guide",
      "author": "Baotong Zheng, Junwei Han",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1 Introduce",
        "2 Example: The inference of the relative abundance matrix of immune cells",
        "3 Example: Use mutation annotation file (MAF) format data to build a binary mutations matrix",
        "4 Example: Identification of somatic mutation-driven immune cells.",
        "5 Example: Visualization"
      ],
      "created": "2020-05-31 11:26:39",
      "modified": "2023-09-04 00:40:18",
      "commits": 12
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "smdic",
  "_universes": [
    "hanjunwei-lab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.6",
      "date": "2026-06-13T08:47:01.000Z",
      "distro": "noble",
      "commit": "70ba7d1dc794c4a4cf862cb7f0d0f75130d68c67",
      "fileid": "https://r2.ropensci.org/12b4761220a1251ee865ff8e509f8292641c19b71bae8c45e6fbac1d7d5ccf91",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/27461858756"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.6",
      "date": "2026-06-13T08:46:56.000Z",
      "distro": "noble",
      "commit": "70ba7d1dc794c4a4cf862cb7f0d0f75130d68c67",
      "fileid": "https://r2.ropensci.org/28c8dfcb71395174bbce053fb4e24d92d3e7ae21583140be9fbdb92da1f71865",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/27461858756"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.6",
      "date": "2026-06-13T08:45:18.000Z",
      "commit": "70ba7d1dc794c4a4cf862cb7f0d0f75130d68c67",
      "fileid": "https://r2.ropensci.org/2742f3f54a6515bb9d491d3ca707f57e743e2025b5af8008484bc45b96da003e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/27461858756"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.6",
      "date": "2026-06-13T08:45:29.000Z",
      "commit": "70ba7d1dc794c4a4cf862cb7f0d0f75130d68c67",
      "fileid": "https://r2.ropensci.org/a178bfb24f9db8724ab99253a601dc0e7dbcb7a4700e35113f05bc9332920703",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/27461858756"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.6",
      "date": "2026-06-13T08:47:04.000Z",
      "commit": "70ba7d1dc794c4a4cf862cb7f0d0f75130d68c67",
      "fileid": "https://r2.ropensci.org/fa2114c9c942036e19f8c54e3d5c4b7f710952a0bb58835cc90ac2862539a412",
      "status": "success",
      "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/27461858756"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.6",
      "date": "2026-06-13T08:45:25.000Z",
      "commit": "70ba7d1dc794c4a4cf862cb7f0d0f75130d68c67",
      "fileid": "https://r2.ropensci.org/99077da7802485487902dac0879a3e75b3f21202d6d8e3659e4586daffe0bebb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/27461858756"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.6",
      "date": "2026-06-13T08:45:38.000Z",
      "commit": "70ba7d1dc794c4a4cf862cb7f0d0f75130d68c67",
      "fileid": "https://r2.ropensci.org/f12198a7d7638b27d2e49f33dfc22327b3c6178964daafc94bc04c5edb14377f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/27461858756"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.6",
      "date": "2026-06-13T08:45:26.000Z",
      "commit": "70ba7d1dc794c4a4cf862cb7f0d0f75130d68c67",
      "fileid": "https://r2.ropensci.org/5cc6163f275b9c4f022407eb71d655ef20988a5fad2a408cd640f4641a5853f8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/27461858756"
    }
  ]
}