{
  "_id": "6ac8c7b9de46216d5edd710b",
  "Package": "diffdriver",
  "Type": "Package",
  "Title": "Identify differential selection",
  "Version": "0.1.8",
  "Authors@R": "c(\nperson(\"Siming\", \"Zhao\", , \"siming.zhao06@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Jie\", \"Zhou\", role = \"aut\"),\nperson(\"Qirui\", \"Zhang\", role = \"aut\")\n)",
  "Maintainer": "Siming Zhao <siming.zhao@dartmouth.edu>",
  "Description": "This package implements a statistical method to detect\ndifferential selection of somatic mutations under different\nenvironments",
  "License": "MIT",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.2",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev",
  "Repository": "https://szhaolab.r-universe.dev",
  "Date/Publication": "2026-07-11 20:23:49 UTC",
  "RemoteUrl": "https://github.com/szhaolab/diffdriver",
  "RemoteRef": "HEAD",
  "RemoteSha": "a47b7dd99b0f1c04e15b5eb2aadaa8d9feea90ad",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-09 10:11:45 UTC",
    "User": "root"
  },
  "Author": "Siming Zhao [aut, cre],\nJie Zhou [aut],\nQirui Zhang [aut]",
  "_user": "szhaolab",
  "_type": "src",
  "_file": "diffdriver_0.1.8.tar.gz",
  "_fileid": "https://r2.ropensci.org/58af23f1ae0b8152d4b166c79ffe0f62d45ffd8c53162d3fab5244949af8ae8c",
  "_filesize": 971355,
  "_sha256": "58af23f1ae0b8152d4b166c79ffe0f62d45ffd8c53162d3fab5244949af8ae8c",
  "_expires": "2027-01-17T10:53:43.000Z",
  "_created": "2026-10-09T10:11:45.000Z",
  "_published": "2026-10-09T10:53:45.098Z",
  "_buildurl": "https://github.com/r-universe/szhaolab/actions/runs/37915707420",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 113772646233,
      "time": 148,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11609004302"
    },
    {
      "job": 113772646180,
      "time": 176,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11608449625"
    },
    {
      "job": 113772646348,
      "time": 166,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11611391913"
    },
    {
      "job": 113772646361,
      "time": 146,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11612355424"
    },
    {
      "job": 113771360975,
      "time": 218,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11608584059"
    },
    {
      "job": 113772646195,
      "time": 130,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11608584374"
    },
    {
      "job": 113772646153,
      "time": 118,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11608824323"
    },
    {
      "job": 113772646152,
      "time": 126,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11609263911"
    },
    {
      "job": 113772646207,
      "time": 105,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11609923568"
    }
  ],
  "_upstream": "https://github.com/szhaolab/diffdriver",
  "_commit": {
    "id": "a47b7dd99b0f1c04e15b5eb2aadaa8d9feea90ad",
    "author": "Siming Zhao <siming.zhao26@gmail.com>",
    "committer": "Siming Zhao <siming.zhao26@gmail.com>",
    "message": "Warn on single-level (zero-variance) covariates\n\nCheck each covariate for variance among the retained samples; any covariate\nwith a single level is dropped with a warning (it carries no information and\nwould make the model rank-deficient, or error in model.matrix for a\nsingle-level factor). If no covariate with variance remains, proceed without\ncovariate adjustment. Document the behavior.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>\n",
    "time": 1783801429
  },
  "_maintainer": {
    "name": "Siming Zhao",
    "email": "siming.zhao@dartmouth.edu",
    "login": "simingz",
    "description": "Assistant Professor at Dartmouth College",
    "uuid": 7595604
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "brglm",
      "role": "Imports"
    },
    {
      "package": "fastTopics",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "logging",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "szhaolab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-07",
      "n": 3
    },
    {
      "week": "2026-12",
      "n": 2
    },
    {
      "week": "2026-26",
      "n": 5
    },
    {
      "week": "2026-27",
      "n": 3
    },
    {
      "week": "2026-28",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "jiezhou-2",
      "count": 198,
      "uuid": 51555963
    },
    {
      "user": "simingz",
      "count": 52,
      "uuid": 7595604
    },
    {
      "user": "atvorundunn",
      "count": 11,
      "uuid": 47759175
    },
    {
      "user": "ld-zhangqr",
      "count": 8,
      "uuid": 90957965
    }
  ],
  "_userbio": {
    "uuid": 89938691,
    "type": "organization",
    "name": "szhaolab",
    "followers": 3
  },
  "_downloads": {
    "count": 385,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/diffdriver"
  },
  "_devurl": "https://github.com/szhaolab/diffdriver",
  "_searchresults": 13,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/diffdriver.html",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/szhaolab/diffdriver",
  "_realowner": "szhaolab",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.7",
      "date": "2026-06-26"
    }
  ],
  "_exports": [
    "ddmodel",
    "ddmodel_binary",
    "ddmodel_binary_simple",
    "diffdriver",
    "genebinom",
    "genefisher",
    "genelr",
    "mlr",
    "mlr.v2",
    "plot_mut"
  ],
  "_help": [
    {
      "page": "ddmcode",
      "title": "Add intercept, if have functtypecode, then code and move to the front. different from driverMAPS! only allows functtypecode =7 ||8 when functypecode is included in selectvars.",
      "topics": [
        "ddmcode"
      ]
    },
    {
      "page": "ddmodel",
      "title": "diffDriver model",
      "topics": [
        "ddmodel"
      ]
    },
    {
      "page": "ddmodel_binary",
      "title": "diffDriver model only for binary phenotype.",
      "topics": [
        "ddmodel_binary"
      ]
    },
    {
      "page": "ddmodel_binary_simple",
      "title": "diffDriver model only for binary phenotype, assuming bmr the same across samples.",
      "topics": [
        "ddmodel_binary_simple"
      ]
    },
    {
      "page": "diffdriver",
      "title": "Run diffDriver with Input Files",
      "topics": [
        "diffdriver"
      ]
    },
    {
      "page": "genebinom",
      "title": "gene level binomial test",
      "topics": [
        "genebinom"
      ]
    },
    {
      "page": "genefisher",
      "title": "gene level fisher's exact test",
      "topics": [
        "genefisher"
      ]
    },
    {
      "page": "genelr",
      "title": "gene level logistic regression",
      "topics": [
        "genelr"
      ]
    },
    {
      "page": "mlr",
      "title": "gene level multiple linear regression",
      "topics": [
        "mlr"
      ]
    },
    {
      "page": "mlr.v2",
      "title": "gene level multiple linear regression, correcting for total number of mutations",
      "topics": [
        "mlr.v2"
      ]
    },
    {
      "page": "optifix",
      "title": "optifix. Optimise with fixed parameters",
      "topics": [
        "optifix"
      ]
    },
    {
      "page": "plot_mut",
      "title": "plot phenotype, mutation and annotation for a gene across samples",
      "topics": [
        "plot_mut"
      ]
    }
  ],
  "_readme": "https://github.com/szhaolab/diffdriver/raw/HEAD/README.md",
  "_rundeps": [
    "ashr",
    "askpass",
    "base64enc",
    "BH",
    "brglm",
    "bslib",
    "cachem",
    "cli",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "digest",
    "dplyr",
    "dqrng",
    "etrunct",
    "evaluate",
    "farver",
    "fastmap",
    "fastTopics",
    "FNN",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "ggrepel",
    "glue",
    "gtable",
    "gtools",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httr",
    "invgamma",
    "irlba",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "Matrix",
    "matrixStats",
    "memoise",
    "mime",
    "mixsqp",
    "openssl",
    "otel",
    "pbapply",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "prettyunits",
    "profileModel",
    "progress",
    "promises",
    "purrr",
    "quadprog",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppParallel",
    "RcppProgress",
    "reshape2",
    "RhpcBLASctl",
    "rlang",
    "rmarkdown",
    "RSpectra",
    "Rtsne",
    "S7",
    "sass",
    "scales",
    "sitmo",
    "SQUAREM",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "truncnorm",
    "utf8",
    "uwot",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "yaml"
  ],
  "_score": 3.989004615698537,
  "_indexed": true,
  "_nocasepkg": "diffdriver",
  "_universes": [
    "szhaolab",
    "simingz"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.8",
      "date": "2026-10-09T10:14:14.000Z",
      "distro": "resolute",
      "commit": "a47b7dd99b0f1c04e15b5eb2aadaa8d9feea90ad",
      "fileid": "https://r2.ropensci.org/203152208d22410e1f9d9898b3f3d92b52049a23d6bd6c4aed84669734159b23",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/szhaolab/actions/runs/37915707420"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.8",
      "date": "2026-10-09T10:14:31.000Z",
      "distro": "resolute",
      "commit": "a47b7dd99b0f1c04e15b5eb2aadaa8d9feea90ad",
      "fileid": "https://r2.ropensci.org/20af4967e228da40f90bbc3170600f18e0a931d0049166c9b99903f9b9fc845c",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/szhaolab/actions/runs/37915707420"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.8",
      "date": "2026-10-09T10:49:46.000Z",
      "commit": "a47b7dd99b0f1c04e15b5eb2aadaa8d9feea90ad",
      "fileid": "https://r2.ropensci.org/e60d99e8e860a87582958166ec63699f6975947372c79d95f01825e6314952b0",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/szhaolab/actions/runs/37915707420"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.8",
      "date": "2026-10-09T10:53:03.000Z",
      "commit": "a47b7dd99b0f1c04e15b5eb2aadaa8d9feea90ad",
      "fileid": "https://r2.ropensci.org/260f0abc875ad043508766fca008e54f70236bedb76d931f5bf76b6c6339879b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/szhaolab/actions/runs/37915707420"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.8",
      "date": "2026-10-09T10:14:19.000Z",
      "commit": "a47b7dd99b0f1c04e15b5eb2aadaa8d9feea90ad",
      "fileid": "https://r2.ropensci.org/e04773ff5da37d865e1a02521bc52ad226ab847fbab10cadd7d99eec2228467b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/szhaolab/actions/runs/37915707420"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.8",
      "date": "2026-10-09T10:13:30.000Z",
      "commit": "a47b7dd99b0f1c04e15b5eb2aadaa8d9feea90ad",
      "fileid": "https://r2.ropensci.org/6a086ada00155e5cb11d64c4f2cd19e59ccee3486cff8f6e126a6a4a858235bf",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/szhaolab/actions/runs/37915707420"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.8",
      "date": "2026-10-09T10:13:38.000Z",
      "commit": "a47b7dd99b0f1c04e15b5eb2aadaa8d9feea90ad",
      "fileid": "https://r2.ropensci.org/b38baffbff14f3229cf3e68367911245659c6d1660c2c7c36bdcb99d7bef2e46",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/szhaolab/actions/runs/37915707420"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.8",
      "date": "2026-10-09T10:13:19.000Z",
      "commit": "a47b7dd99b0f1c04e15b5eb2aadaa8d9feea90ad",
      "fileid": "https://r2.ropensci.org/a68ecdaffff7643473d1e6c224dece67da2ee59e4f1b4e7d54faa3e05b7cd5fa",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/szhaolab/actions/runs/37915707420"
    }
  ]
}