{
  "_id": "6a17ea3facfb0bcc41da2abe",
  "Package": "DeepTarget",
  "Type": "Package",
  "Title": "Deep characterization of cancer drugs",
  "Version": "1.7.0",
  "Authors@R": "c(\nperson(\"Sanju\", \"Sinha\", email = \"sanju@terpmail.umd.edu\", role =\"aut\"),\nperson(\"Trinh\", \"Nguyen\", email = \"tinh.nguyen@nih.gov\", role = c(\"aut\",\"cre\"),comment=c(ORCID=\"0000-0002-6606-6948\")),\nperson(\"Ying\", \"Hu\", email = \"yhu@mail.nih.gov\", role =\"aut\"))",
  "Description": "This package predicts a drug’s primary target(s) or\nsecondary target(s) by integrating large-scale genetic and drug\nscreens from the Cancer Dependency Map project run by the Broad\nInstitute. It further investigates whether the drug\nspecifically targets the wild-type or mutated target forms. To\nshow how to use this package in practice, we provided sample\ndata along with step-by-step example.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "biocViews": "GeneTarget, GenePrediction,Pathways, GeneExpression, RNASeq,\nImmunoOncology,DifferentialExpression, GeneSetEnrichment,\nReportWriting,CRISPR",
  "RoxygenNote": "7.2.3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libssl-dev\nlibx11-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:03:17 UTC",
  "RemoteUrl": "https://github.com/bioc/DeepTarget",
  "RemoteRef": "HEAD",
  "RemoteSha": "824a47300af889b4dca4a93f2720f7b9537dfe41",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 06:27:33 UTC",
    "User": "root"
  },
  "Author": "Sanju Sinha [aut],\nTrinh Nguyen [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-6606-6948>),\nYing Hu [aut]",
  "Maintainer": "Trinh Nguyen <tinh.nguyen@nih.gov>",
  "MD5sum": "bcf1294d815a326d4e12d13be761b3de",
  "_user": "bioc",
  "_type": "src",
  "_file": "DeepTarget_1.7.0.tar.gz",
  "_fileid": "904597beac712b50ec6979ae73fa2ab82ca18b06833b0b9e745d20a758af05c3",
  "_filesize": 2776220,
  "_sha256": "904597beac712b50ec6979ae73fa2ab82ca18b06833b0b9e745d20a758af05c3",
  "_created": "2026-05-28T06:27:33.000Z",
  "_published": "2026-05-28T07:09:51.277Z",
  "_jobs": [
    {
      "job": 78236037064,
      "time": 204,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7259175920"
    },
    {
      "job": 78236037145,
      "time": 377,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7259219742"
    },
    {
      "job": 78236037115,
      "time": 359,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259215061"
    },
    {
      "job": 78236037090,
      "time": 229,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7259189740"
    },
    {
      "job": 78236037062,
      "time": 186,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259180656"
    },
    {
      "job": 78235491544,
      "time": 281,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259126370"
    },
    {
      "job": 78236037085,
      "time": 175,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259169006"
    },
    {
      "job": 78236037131,
      "time": 2486,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7259751201"
    },
    {
      "job": 78236037095,
      "time": 696,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7259299324"
    },
    {
      "job": 78236037089,
      "time": 830,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259331991"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26558454684",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/DeepTarget",
  "_commit": {
    "id": "824a47300af889b4dca4a93f2720f7b9537dfe41",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381397
  },
  "_maintainer": {
    "name": "Trinh Nguyen",
    "email": "tinh.nguyen@nih.gov",
    "login": "trinhnguyenp",
    "description": "",
    "uuid": 50640811,
    "orcid": "0000-0002-6606-6948"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2.0",
      "role": "Depends"
    },
    {
      "package": "fgsea",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "pROC",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "depmap",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.7.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.6.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "genetarget",
    "geneprediction",
    "pathways",
    "geneexpression",
    "rnaseq",
    "immunooncology",
    "differentialexpression",
    "genesetenrichment",
    "reportwriting",
    "crispr"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 256,
    "source": "https://www.bioconductor.org/packages/stats/bioc/DeepTarget"
  },
  "_searchresults": 3,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DeepTarget.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "computeCor",
    "Depmap2DeepTarget",
    "DMB",
    "DoInteractExp",
    "DoInteractMutant",
    "DoPWY",
    "DTR",
    "plotCor",
    "plotSim",
    "PredMaxSim",
    "PredTarget"
  ],
  "_datasets": [
    {
      "name": "OntargetM",
      "title": "An object containing a small part of the data from the Cancer Dependency Map (depmap.org) to demonstrate in DeepTarget pipeline",
      "object": "OntargetM",
      "file": "OntargetM.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "computeCor",
      "title": "Compute a correlation between the every gene vs each drug response",
      "topics": [
        "computeCor"
      ]
    },
    {
      "page": "Depmap2DeepTarget",
      "title": "Retrieval and preparation of input data required from Depmap to Deeptarget package.",
      "topics": [
        "Depmap2DeepTarget"
      ]
    },
    {
      "page": "DMB",
      "title": "Predicting Drug Mutant Binding for mutant or non-mutant form",
      "topics": [
        "DMB"
      ]
    },
    {
      "page": "DoInteractExp",
      "title": "Compute the interaction between the drug and KO expression",
      "topics": [
        "DoInteractExp"
      ]
    },
    {
      "page": "DoInteractMutant",
      "title": "Compute interaction between the drug and KO expression in term of mutant vs non-mutant",
      "topics": [
        "DoInteractMutant"
      ]
    },
    {
      "page": "DoPWY",
      "title": "Provide a probability score for each pathway for the primary of mechanism of action (MOA) of a drug",
      "topics": [
        "DoPWY"
      ]
    },
    {
      "page": "DTR",
      "title": "Predicting Drug Target Response (DTR) for primary or secondary targets",
      "topics": [
        "DTR"
      ]
    },
    {
      "page": "OntargetM",
      "title": "An object containing a small part of the data from the Cancer Dependency Map (depmap.org) to demonstrate in DeepTarget pipeline",
      "topics": [
        "OntargetM"
      ]
    },
    {
      "page": "plotCor",
      "title": "Plot the correlation",
      "topics": [
        "plotCor"
      ]
    },
    {
      "page": "plotSim",
      "title": "Plot the similarty between corelation values and P vals for all genes. The top 5 genes are labeled.",
      "topics": [
        "plotSim"
      ]
    },
    {
      "page": "PredMaxSim",
      "title": "Predict the most similar gene to the drug response",
      "topics": [
        "PredMaxSim"
      ]
    },
    {
      "page": "PredTarget",
      "title": "Prediction of the most similar known targeted gene.",
      "topics": [
        "PredTarget"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/DeepTarget/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationHub",
    "askpass",
    "backports",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocManager",
    "BiocParallel",
    "BiocVersion",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "boot",
    "broom",
    "cachem",
    "car",
    "carData",
    "cli",
    "clipr",
    "codetools",
    "colorspace",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "depmap",
    "Deriv",
    "doBy",
    "dplyr",
    "ExperimentHub",
    "farver",
    "fastmap",
    "fastmatch",
    "fgsea",
    "filelock",
    "forecast",
    "formatR",
    "Formula",
    "fracdiff",
    "futile.logger",
    "futile.options",
    "generics",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "glue",
    "gridExtra",
    "gtable",
    "hms",
    "httr",
    "httr2",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "memoise",
    "mgcv",
    "microbenchmark",
    "mime",
    "minqa",
    "modelr",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "openssl",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "png",
    "polynom",
    "prettyunits",
    "pROC",
    "progress",
    "purrr",
    "quantreg",
    "R6",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "readr",
    "reformulas",
    "rlang",
    "RSQLite",
    "rstatix",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseM",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "tzdb",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "XVector",
    "yaml",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "DeepTarget_Vignette.Rmd",
      "filename": "DeepTarget_Vignette.html",
      "title": "Workflow Demonstration for Deep characterization of cancer drugs",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Part I: Core Analysis",
        "Data Loading and Preparation",
        "Computing Similarity Between Drug Treatment and Gene Knockout",
        "Predicting Similarity Across Known Targeted Genes and All Genes",
        "Computing the Interaction",
        "Interaction Assessment",
        "Preparation for Output",
        "In addition to the output of prediction object, we also identify drugs with low primary target expressing cell lines",
        "Calculating Drug KO Similarities in cell lines with low primary target",
        "Part II: Application",
        "Finding and visualizing a drug primary target",
        "Predicting whether the drug specifically targets the wild-type or mutated target forms",
        "Predicting secondary target(s) that mediate its response when the primary target is not expressed",
        "Part III: Conclusion",
        "Session info"
      ],
      "created": "2023-11-30 19:57:44",
      "modified": "2024-10-21 14:03:16",
      "commits": 6
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "deeptarget",
  "_universes": [
    "bioc",
    "trinhnguyenp"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.7.0",
      "date": "2026-05-28T06:31:40.000Z",
      "distro": "noble",
      "commit": "824a47300af889b4dca4a93f2720f7b9537dfe41",
      "fileid": "2cc8d5ce2e52052dfcddd63db576de7c3411fcbd1ac254473940ddd1c9badc98",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558454684"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.7.0",
      "date": "2026-05-28T06:31:20.000Z",
      "distro": "noble",
      "commit": "824a47300af889b4dca4a93f2720f7b9537dfe41",
      "fileid": "c673638f81f08272141d742a799a4a7895a023b2e030e2b3e620260fead99952",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558454684"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.7.0",
      "date": "2026-05-28T06:30:08.000Z",
      "commit": "824a47300af889b4dca4a93f2720f7b9537dfe41",
      "fileid": "4c77b9ceffa5f7e67cc7e12bee38ebf60c1419a639814d8e8c4e566e56a1f1dd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558454684"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.7.0",
      "date": "2026-05-28T06:30:06.000Z",
      "commit": "824a47300af889b4dca4a93f2720f7b9537dfe41",
      "fileid": "250d30542087e3f8ced98661789f25991d6ab864f6b5952a36b2c4291e85e05e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558454684"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.7.0",
      "date": "2026-05-28T06:30:56.000Z",
      "commit": "824a47300af889b4dca4a93f2720f7b9537dfe41",
      "fileid": "eb9a087855e470e1736ad0fa566f804a830163a52c6ddbc41b42924751d036c9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558454684"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-05-28T06:34:22.000Z",
      "commit": "824a47300af889b4dca4a93f2720f7b9537dfe41",
      "fileid": "e363fd6171d78d26c26c90bf275beb73421d0c6419f4df825801316affa703bc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558454684"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-05-28T06:34:07.000Z",
      "commit": "824a47300af889b4dca4a93f2720f7b9537dfe41",
      "fileid": "fba6fee5cae5aa43cd839b7842f12f815dc92d420b3caa180f10639935d0bd98",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558454684"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-05-28T06:35:18.000Z",
      "commit": "824a47300af889b4dca4a93f2720f7b9537dfe41",
      "fileid": "1390a8b25645b1791fb8d9c7f29cde8436fcac4475e918f76427797596ee0487",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558454684"
    }
  ]
}