{
  "_id": "6a3bb1105cdecea1d682b52c",
  "Package": "drugfindR",
  "Title": "Investigate iLINCS for candidate repurposable drugs",
  "Version": "1.1.0",
  "Authors@R": "c(\nperson(given = c(\"Ali\", \"Sajid\"),\nfamily = \"Imami\",\nrole = c(\"aut\", \"cre\"),\nemail = \"Ali.Sajid.Imami@gmail.com\",\ncomment = c(ORCID = \"0000-0003-3684-3539\")),\nperson(given = c(\"Smita\"),\nfamily = \"Sahay\",\nrole = c(\"aut\"),\nemail = \"Smita.Sahay@rockets.utoledo.edu\",\ncomment = c(ORCID = \"0009-0003-4377-8963\")),\nperson(given = c(\"Justin\", \"Fortune\"),\nfamily = \"Creeden\",\nrole = c(\"aut\"),\nemail = \"Justin.Creeden@rockets.utoledo.edu\",\ncomment = c(ORCID = \"0000-0003-3123-8401\")),\nperson(given = c(\"Robert\", \"Erne\"),\nfamily = \"McCullumsmith\",\nrole = c(\"ctb\", \"fnd\"),\nemail = \"Robert.McCullumsmith@utoledo.edu\",\ncomment = c(ORCID = \"0000-0001-6921-7150\"))\n)",
  "Description": "This package provides a convenient way to access the LINCS\nSignatures available in the iLINCS database. These signatures\ninclude Consensus Gene Knockdown Signatures, Gene\nOverexpression signatures and Chemical Perturbagen Signatures.\nIt also provides a way to enter your own transcriptomic\nsignatures and identify concordant and discordant signatures in\nthe LINCS database.",
  "License": "GPL-3 + file LICENSE",
  "Encoding": "UTF-8",
  "URL": "https://github.com/CogDisResLab/drugfindR,\nhttps://cogdisreslab.github.io/drugfindR/",
  "BugReports": "https://github.com/CogDisResLab/drugfindR/issues",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "biocViews": "FunctionalPrediction, DifferentialExpression,\nGeneSetEnrichment, SingleCell, Network",
  "Config/testthat/edition": "3",
  "Config/testthat/parallel": "true",
  "VignetteBuilder": "knitr",
  "Collate": "'utilities.R' 'consensusConcordants.R' 'drugfindR-package.R'\n'filterSignature.R' 'getConcordants.R' 'getSignature.R'\n'prepareSignature.R' 'investigateSignature.R'\n'investigateTarget.R'",
  "Config/pak/sysreqs": "libicu-dev libssl-dev libx11-dev",
  "Repository": "https://cogdisreslab.r-universe.dev",
  "Date/Publication": "2026-06-24 10:08:12 UTC",
  "RemoteUrl": "https://github.com/CogDisResLab/drugfindR",
  "RemoteRef": "HEAD",
  "RemoteSha": "93f378d37012133374de77daaead03ac52dcb6db",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-24 10:22:29 UTC",
    "User": "root"
  },
  "Author": "Ali Sajid Imami [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3684-3539>),\nSmita Sahay [aut] (ORCID: <https://orcid.org/0009-0003-4377-8963>),\nJustin Fortune Creeden [aut] (ORCID:\n<https://orcid.org/0000-0003-3123-8401>),\nRobert Erne McCullumsmith [ctb, fnd] (ORCID:\n<https://orcid.org/0000-0001-6921-7150>)",
  "Maintainer": "Ali Sajid Imami <Ali.Sajid.Imami@gmail.com>",
  "MD5sum": "4e23f8868f0e3fd37735a63534a1b7be",
  "_user": "cogdisreslab",
  "_type": "src",
  "_file": "drugfindR_1.1.0.tar.gz",
  "_fileid": "6247a530831b733bd8f96c20504cada677e37b9ef5ee34b00d2e90856a7fb233",
  "_filesize": 2090966,
  "_sha256": "6247a530831b733bd8f96c20504cada677e37b9ef5ee34b00d2e90856a7fb233",
  "_created": "2026-06-24T10:22:29.000Z",
  "_published": "2026-06-24T10:27:28.905Z",
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 83171481415,
      "time": 224,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7846813941"
    },
    {
      "job": 83171481404,
      "time": 229,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7846815988"
    },
    {
      "job": 83171481390,
      "time": 187,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7846829282"
    },
    {
      "job": 83171481466,
      "time": 186,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7846828473"
    },
    {
      "job": 83170691761,
      "time": 273,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7846733023"
    },
    {
      "job": 83171481382,
      "time": 171,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7846795608"
    },
    {
      "job": 83171481450,
      "time": 155,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7846789634"
    },
    {
      "job": 83171481408,
      "time": 160,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7846791092"
    },
    {
      "job": 83171481444,
      "time": 161,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7846791787"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28091582071",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/CogDisResLab/drugfindR",
  "_commit": {
    "id": "93f378d37012133374de77daaead03ac52dcb6db",
    "author": "renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "chore(deps): update r-lib/actions action to v2.12.1 (#198)\n\nCo-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>",
    "time": 1782295692
  },
  "_maintainer": {
    "name": "Ali Sajid Imami",
    "email": "ali.sajid.imami@gmail.com",
    "login": "alisajid",
    "orcid": "0000-0003-3684-3539",
    "twitter": "@doctor_no",
    "description": "",
    "uuid": 395482
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "lifecycle",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "httr2",
      "role": "Imports"
    },
    {
      "package": "curl",
      "role": "Imports"
    },
    {
      "package": "DFplyr",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "biocthis",
      "role": "Suggests"
    },
    {
      "package": "codemetar",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "here",
      "role": "Suggests"
    },
    {
      "package": "httptest2",
      "role": "Suggests"
    },
    {
      "package": "jsonlite",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    },
    {
      "package": "usethis",
      "role": "Suggests"
    }
  ],
  "_owner": "cogdisreslab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2025-33",
      "n": 4
    },
    {
      "week": "2025-41",
      "n": 2
    },
    {
      "week": "2025-42",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 1
    },
    {
      "week": "2025-47",
      "n": 3
    },
    {
      "week": "2025-48",
      "n": 33
    },
    {
      "week": "2025-49",
      "n": 12
    },
    {
      "week": "2025-50",
      "n": 8
    },
    {
      "week": "2025-51",
      "n": 3
    },
    {
      "week": "2026-03",
      "n": 3
    },
    {
      "week": "2026-04",
      "n": 1
    },
    {
      "week": "2026-05",
      "n": 1
    },
    {
      "week": "2026-06",
      "n": 7
    },
    {
      "week": "2026-07",
      "n": 1
    },
    {
      "week": "2026-08",
      "n": 1
    },
    {
      "week": "2026-09",
      "n": 1
    },
    {
      "week": "2026-13",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-23",
      "n": 6
    },
    {
      "week": "2026-25",
      "n": 1
    },
    {
      "week": "2026-26",
      "n": 2
    }
  ],
  "_tags": [
    {
      "name": "v0.99.1266",
      "date": "2025-11-12"
    },
    {
      "name": "v0.99.1267",
      "date": "2025-11-12"
    },
    {
      "name": "v0.99.1268",
      "date": "2025-11-12"
    },
    {
      "name": "v0.99.1269",
      "date": "2025-11-12"
    },
    {
      "name": "v0.99.1292",
      "date": "2025-11-30"
    },
    {
      "name": "v0.99.1293",
      "date": "2025-11-30"
    },
    {
      "name": "v0.99.1299",
      "date": "2025-12-01"
    },
    {
      "name": "v0.99.1295",
      "date": "2025-12-02"
    },
    {
      "name": "v0.99.1302",
      "date": "2025-12-02"
    },
    {
      "name": "v0.99.1303",
      "date": "2025-12-02"
    },
    {
      "name": "v0.99.1304",
      "date": "2025-12-02"
    },
    {
      "name": "v0.99.1329",
      "date": "2025-12-12"
    },
    {
      "name": "v0.99.1335",
      "date": "2025-12-14"
    },
    {
      "name": "v0.99.1336",
      "date": "2025-12-14"
    },
    {
      "name": "v0.99.1316",
      "date": "2025-12-15"
    },
    {
      "name": "v0.99.1344",
      "date": "2025-12-16"
    },
    {
      "name": "v0.99.1346",
      "date": "2025-12-16"
    },
    {
      "name": "v0.99.1349",
      "date": "2026-01-12"
    },
    {
      "name": "v0.99.1170",
      "date": "2026-01-28"
    },
    {
      "name": "v0.99.1361",
      "date": "2026-01-29"
    },
    {
      "name": "v0.99.1363",
      "date": "2026-01-29"
    },
    {
      "name": "v0.99.1369",
      "date": "2026-02-07"
    },
    {
      "name": "v0.99.1370",
      "date": "2026-02-07"
    },
    {
      "name": "v0.99.1371",
      "date": "2026-02-07"
    },
    {
      "name": "v0.99.2516",
      "date": "2026-02-15"
    }
  ],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.1.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.0.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "lincs",
    "ilincs",
    "drug repurposing",
    "drug discovery",
    "transcriptomics",
    "gene expression",
    "gene knockdown",
    "gene\noverexpression",
    "chemical perturbagen",
    "drugfindr",
    "bioinformatics",
    "bioinformatics-pipeline"
  ],
  "_stars": 11,
  "_contributors": [
    {
      "user": "alisajid",
      "count": 1073,
      "uuid": 395482
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 83421213,
    "type": "organization",
    "name": "Cognitive Disorders Research Lab",
    "followers": 7
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/drugfindR"
  },
  "_devurl": "https://github.com/cogdisreslab/drugfindr",
  "_pkgdown": "https://cogdisreslab.github.io/drugfindR/",
  "_searchresults": 159,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/drugfindR.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/cogdisreslab/drugfindr",
  "_realowner": "bioc",
  "_cranurl": true,
  "_exports": [
    "consensusConcordants",
    "filterSignature",
    "getConcordants",
    "getSignature",
    "investigateSignature",
    "investigateTarget",
    "prepareSignature"
  ],
  "_help": [
    {
      "page": "consensusConcordants",
      "title": "Generate a Consensus list of Targets *[Stable]*",
      "topics": [
        "consensusConcordants"
      ]
    },
    {
      "page": "filterSignature",
      "title": "Filter the L1000 Signature *[Stable]*",
      "topics": [
        "filterSignature"
      ]
    },
    {
      "page": "getConcordants",
      "title": "Get concordant signatures from iLINCS database *[Stable]*",
      "topics": [
        "getConcordants"
      ]
    },
    {
      "page": "getSignature",
      "title": "Get the L1000 Signature from iLINCS *[Stable]*",
      "topics": [
        "getSignature"
      ]
    },
    {
      "page": "investigateSignature",
      "title": "Investigate a given DGE dataset *[Stable]*",
      "topics": [
        "investigateSignature"
      ]
    },
    {
      "page": "investigateTarget",
      "title": "Investigate concordant signatures for a gene or drug *[Stable]*",
      "topics": [
        "investigateTarget"
      ]
    },
    {
      "page": "prepareSignature",
      "title": "Prepare an L1000 Signature from a given differential gene expression output *[Stable]*",
      "topics": [
        "prepareSignature"
      ]
    }
  ],
  "_readme": "https://github.com/CogDisResLab/drugfindR/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "BiocGenerics",
    "bit",
    "bit64",
    "cli",
    "clipr",
    "cpp11",
    "crayon",
    "curl",
    "DFplyr",
    "dplyr",
    "generics",
    "glue",
    "hms",
    "httr2",
    "lifecycle",
    "magrittr",
    "openssl",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "readr",
    "rlang",
    "S4Vectors",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "drugfindR.Rmd",
      "filename": "drugfindR.html",
      "title": "drugfindR",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Use Cases",
        "Package Design",
        "Pipeline Components",
        "Use Case 1: Identifying Candidate Drugs from an Input Signature",
        "Step 1: Get the Signature",
        "Step 2: Prepare the Signature",
        "Step 3: Filter the Signature",
        "Step 4: Get the Concordant Signatures",
        "Step 5: Get the list of Consensus Concordant Signatures",
        "Alternate One-Step Method",
        "Environment Setup"
      ],
      "created": "2023-01-29 05:18:26",
      "modified": "2025-12-14 22:00:30",
      "commits": 21
    }
  ],
  "_score": 7.284182494636902,
  "_indexed": false,
  "_nocasepkg": "drugfindr",
  "_universes": [
    "cogdisreslab"
  ],
  "_indexurl": "https://bioc.r-universe.dev/drugfindR",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-06-24T10:25:23.000Z",
      "distro": "resolute",
      "commit": "93f378d37012133374de77daaead03ac52dcb6db",
      "fileid": "ecaf7a3d5dad3509ed1cf566210c7ef2f5f05af61674227873addd4490b5073a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28091582071"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-06-24T10:25:20.000Z",
      "distro": "resolute",
      "commit": "93f378d37012133374de77daaead03ac52dcb6db",
      "fileid": "78c904512a46b0fd2c32ec8710f30a82103907b569b20bde19f2e845c57885c2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28091582071"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-06-24T10:25:54.000Z",
      "commit": "93f378d37012133374de77daaead03ac52dcb6db",
      "fileid": "6fd695dc52ef546aa6ace727f5a145ee1ca60e2ac57dd3cc88c260eab941f87f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28091582071"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-06-24T10:25:47.000Z",
      "commit": "93f378d37012133374de77daaead03ac52dcb6db",
      "fileid": "cd79925e9973163e575161bd6e113916fe520bfd65cfba5444220e18363ef29f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28091582071"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-06-24T10:25:40.000Z",
      "commit": "93f378d37012133374de77daaead03ac52dcb6db",
      "fileid": "011d5a2e979bb44ab6fb2549f61651de2f4edbd1a9964e9a3b867f1b3ded50c7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28091582071"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-06-24T10:23:51.000Z",
      "commit": "93f378d37012133374de77daaead03ac52dcb6db",
      "fileid": "53405bbfa4a1e80eab49e2e77ac6a07a29f0d28ca162ea470cea53ca5e0c7869",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28091582071"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-06-24T10:23:56.000Z",
      "commit": "93f378d37012133374de77daaead03ac52dcb6db",
      "fileid": "1c16fec18ac6fcf12d0fa00fd6b0f1106fe1b61f443c9e96a0a66cb02d104726",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28091582071"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-06-24T10:24:09.000Z",
      "commit": "93f378d37012133374de77daaead03ac52dcb6db",
      "fileid": "3591f77bdc2e290f718a5babe967c79980f2e69eae6c2b2ca97953b407ec1507",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28091582071"
    }
  ]
}