{ "_id": "6a1adce91d7bb097a09ea87e", "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://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:06:11 UTC", "RemoteUrl": "https://github.com/bioc/drugfindR", "RemoteRef": "HEAD", "RemoteSha": "8b653fc88529ccd468e21a659224a289a93ee17a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:14:13 UTC", "User": "root" }, "Author": "Ali Sajid Imami [aut, cre] (ORCID:\n),\nSmita Sahay [aut] (ORCID: ),\nJustin Fortune Creeden [aut] (ORCID:\n),\nRobert Erne McCullumsmith [ctb, fnd] (ORCID:\n)", "Maintainer": "Ali Sajid Imami ", "MD5sum": "022c221359ac6e10f5695837d1fabd03", "_user": "bioc", "_type": "src", "_file": "drugfindR_1.1.0.tar.gz", "_fileid": "44c103f3da6e179dd8e9747363422ea9d7681abf87f6df140e9f19e6c4ed9b10", "_filesize": 2087242, "_sha256": "44c103f3da6e179dd8e9747363422ea9d7681abf87f6df140e9f19e6c4ed9b10", "_created": "2026-05-30T09:14:13.000Z", "_published": "2026-05-30T12:49:45.027Z", "_jobs": [ { "job": 78638962215, "time": 191, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307146470" }, { "job": 78638962220, "time": 263, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307152930" }, { "job": 78638962223, "time": 299, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307155785" }, { "job": 78638962216, "time": 141, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7308296400" }, { "job": 78638962212, "time": 161, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7308297773" }, { "job": 78638690464, "time": 307, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307098947" }, { "job": 78638962213, "time": 137, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307141406" }, { "job": 78638962272, "time": 142, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7307142282" }, { "job": 78638962249, "time": 179, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7307145731" }, { "job": 78638962222, "time": 151, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7307143016" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26631996393", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/drugfindR", "_commit": { "id": "8b653fc88529ccd468e21a659224a289a93ee17a", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381571 }, "_maintainer": { "name": "Ali Sajid Imami", "email": "ali.sajid.imami@gmail.com", "login": "alisajid", "orcid": "0000-0003-3684-3539", "twitter": "@doctor_no", "description": "", "uuid": 395482 }, "_distro": "noble", "_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": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-22", "n": 1 }, { "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 } ], "_tags": [], "_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": 10, "_contributors": [ { "user": "alisajid", "count": 1073, "uuid": 395482 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 179, "source": "https://www.bioconductor.org/packages/stats/bioc/drugfindR" }, "_devurl": "https://github.com/cogdisreslab/drugfindr", "_pkgdown": "https://cogdisreslab.github.io/drugfindR/", "_searchresults": 151, "_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", "manual.pdf" ], "_homeurl": "https://github.com/cogdisreslab/drugfindr", "_realowner": "bioc", "_cranurl": false, "_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/bioc/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": 7.17897694729317, "_indexed": true, "_nocasepkg": "drugfindr", "_universes": [ "bioc", "alisajid", "cogdisreslab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.0", "date": "2026-05-30T09:22:49.000Z", "distro": "noble", "commit": "8b653fc88529ccd468e21a659224a289a93ee17a", "fileid": "de99ff2705c560e20980ad99bef3bb9dd183eb22248eaff794fa8abf8f168e27", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631996393" }, { "r": "4.6.0", "os": "linux", "version": "1.1.0", "date": "2026-05-30T09:23:14.000Z", "distro": "noble", "commit": "8b653fc88529ccd468e21a659224a289a93ee17a", "fileid": "76b5ae25ecd8de96f0719a6e0f1463a17389637b412887c737ca380abeba201c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631996393" }, { "r": "4.5.3", "os": "mac", "version": "1.1.0", "date": "2026-05-30T12:48:08.000Z", "commit": "8b653fc88529ccd468e21a659224a289a93ee17a", "fileid": "d42b7e6b63817b75e294c449b2049d4ae0a707559e3813db4446ee1f916fadf5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631996393" }, { "r": "4.6.0", "os": "mac", "version": "1.1.0", "date": "2026-05-30T12:48:06.000Z", "commit": "8b653fc88529ccd468e21a659224a289a93ee17a", "fileid": "47bfd06cb7dd1d8ceb44cd8de4d9372367ebfa14a9db77c05fb977652772b82f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631996393" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.0", "date": "2026-05-30T09:21:57.000Z", "commit": "8b653fc88529ccd468e21a659224a289a93ee17a", "fileid": "9d23b0944de2f66912a7d26d9993c86c628682e07f7b4df437e3b3cad6176bf0", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631996393" }, { "r": "4.7.0", "os": "win", "version": "1.1.0", "date": "2026-05-30T09:20:47.000Z", "commit": "8b653fc88529ccd468e21a659224a289a93ee17a", "fileid": "d8dd678c257f1b5cda829d1398acdea7809ba11fd692e55e00391f4403b920ec", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631996393" }, { "r": "4.5.3", "os": "win", "version": "1.1.0", "date": "2026-05-30T09:21:08.000Z", "commit": "8b653fc88529ccd468e21a659224a289a93ee17a", "fileid": "f157eca45587a196e4836cc3614cd56a33ddf228f019dd71bb5607e488eebfc1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631996393" }, { "r": "4.6.0", "os": "win", "version": "1.1.0", "date": "2026-05-30T09:20:47.000Z", "commit": "8b653fc88529ccd468e21a659224a289a93ee17a", "fileid": "0f782d455a126a6eb8fa36c80719861730c62b65d793f8ff14acca969df92053", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631996393" } ] }