{
  "_id": "6ac4dbb5f511ae58c09a25b1",
  "Package": "RHybridFinder",
  "Type": "Package",
  "Title": "Identification of Hybrid Peptides in Immunopeptidomic Analyses",
  "Version": "0.2.0",
  "Authors@R": "c(person(\"Frederic\", \"Saab\", role = c(\"aut\", \"cre\"),\nemail = \"frederic.saab@umontreal.ca\"),\nperson(\"Peter\", \"Kubiniok\", role = \"aut\") )",
  "Maintainer": "Frederic Saab <frederic.saab@umontreal.ca>",
  "Description": "Tool for the analysis Mass Spectrometry (MS) data in the\ncontext of immunopeptidomic analysis for the identification of\nhybrid peptides and the predictions of binding affinity of all\npeptides using 'netMHCpan' <doi:10.1093/nar/gkaa379> while\nproviding a summary of the netMHCpan output. 'RHybridFinder'\n(RHF) is destined for researchers who are looking to analyze\ntheir MS data for the purpose of identification of potential\nspliced peptides. This package, developed mainly in base R, is\nbased on the workflow published by Faridi et al. in 2018\n<doi:10.1126/sciimmunol.aar3947>.",
  "VignetteBuilder": "knitr",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.1.1",
  "NeedsCompilation": "no",
  "LazyData": "True",
  "LazyDataCompression": "bzip2",
  "Packaged": {
    "Date": "2026-10-06 11:27:17 UTC",
    "User": "root"
  },
  "Author": "Frederic Saab [aut, cre], Peter Kubiniok [aut]",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2021-08-17 15:30:24 UTC",
  "RemoteUrl": "https://github.com/cran/RHybridFinder",
  "RemoteRef": "HEAD",
  "RemoteSha": "3a89236619fc5f249a816ae80fd4ea35daf251df",
  "_user": "cran",
  "_type": "src",
  "_file": "RHybridFinder_0.2.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/7af765b43690b8f303febf618b06811a0a5b8ebec98798f967fac5e869593b3a",
  "_filesize": 1216065,
  "_sha256": "7af765b43690b8f303febf618b06811a0a5b8ebec98798f967fac5e869593b3a",
  "_expires": "2027-01-14T11:29:55.000Z",
  "_created": "2026-10-06T11:27:17.000Z",
  "_published": "2026-10-06T11:29:57.265Z",
  "_jobs": [
    {
      "job": 112245451817,
      "time": 121,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11408489771"
    },
    {
      "job": 112245451876,
      "time": 117,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11408734785"
    },
    {
      "job": 112244426800,
      "time": 164,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11408869243"
    },
    {
      "job": 112245451842,
      "time": 103,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11409129434"
    },
    {
      "job": 112245451902,
      "time": 75,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11409808446"
    },
    {
      "job": 112245451823,
      "time": 85,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11408829581"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/37456187478",
  "_status": "success",
  "_upstream": "https://github.com/cran/RHybridFinder",
  "_commit": {
    "id": "3a89236619fc5f249a816ae80fd4ea35daf251df",
    "author": "Frederic Saab <frederic.saab@umontreal.ca>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.2.0\n",
    "time": 1629214224
  },
  "_maintainer": {
    "name": "Frederic Saab",
    "email": "frederic.saab@umontreal.ca"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "seqinr",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "followers": 630,
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 275,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RHybridFinder"
  },
  "_searchresults": 5,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/RHybridFinder.html",
    "LICENSE"
  ],
  "_realowner": "cran",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2021-06-21"
    },
    {
      "version": "0.2.0",
      "date": "2021-08-17"
    }
  ],
  "_exports": [
    "checknetMHCpan",
    "export_checknetmhcpan_results",
    "export_HybridFinder_results",
    "export_step2_results",
    "HybridFinder",
    "mhc_check",
    "step2_wo_netMHCpan"
  ],
  "_datasets": [
    {
      "name": "db_Human_Liver_AUTD17",
      "title": "db_Human_Liver_AUTD17",
      "object": "db_Human_Liver_AUTD17",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Peptide",
        "X.10lgP",
        "Mass",
        "Length",
        "ppm",
        "m.z",
        "Z",
        "RT",
        "Area",
        "Fraction",
        "Id",
        "Scan",
        "from.Chimera",
        "Source.File",
        "Accession",
        "PTM",
        "AScore",
        "Found.By"
      ],
      "rows": 6108,
      "table": true,
      "tojson": true
    },
    {
      "name": "db_rerun_Human_Liver_AUTD17",
      "title": "db_rerun_Human_Liver_AUTD17",
      "object": "db_rerun_Human_Liver_AUTD17",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Peptide",
        "X.10lgP",
        "Mass",
        "Length",
        "ppm",
        "m.z",
        "Z",
        "RT",
        "Area",
        "Fraction",
        "Id",
        "Scan",
        "from.Chimera",
        "Source.File",
        "Accession",
        "PTM",
        "AScore",
        "Found.By"
      ],
      "rows": 6315,
      "table": true,
      "tojson": true
    },
    {
      "name": "denovo_Human_Liver_AUTD17",
      "title": "denovo_Human_Liver_AUTD17",
      "object": "denovo_Human_Liver_AUTD17",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Fraction",
        "Source.File",
        "Feature",
        "Peptide",
        "Scan",
        "Tag.length",
        "Denovo.score",
        "ALC....",
        "Length",
        "m.z",
        "z",
        "RT",
        "Predict.RT",
        "Mass",
        "ppm",
        "local.confidence....",
        "tag....0..",
        "mode"
      ],
      "rows": 50114,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "checknetMHCpan",
      "title": "checknetMHCpan",
      "topics": [
        "checknetMHCpan"
      ]
    },
    {
      "page": "db_Human_Liver_AUTD17",
      "title": "db_Human_Liver_AUTD17",
      "topics": [
        "db_Human_Liver_AUTD17"
      ]
    },
    {
      "page": "db_rerun_Human_Liver_AUTD17",
      "title": "db_rerun_Human_Liver_AUTD17",
      "topics": [
        "db_rerun_Human_Liver_AUTD17"
      ]
    },
    {
      "page": "denovo_Human_Liver_AUTD17",
      "title": "denovo_Human_Liver_AUTD17",
      "topics": [
        "denovo_Human_Liver_AUTD17"
      ]
    },
    {
      "page": "export_checknetmhcpan_results",
      "title": "export_checknetmhcpan_results",
      "topics": [
        "export_checknetmhcpan_results"
      ]
    },
    {
      "page": "export_results",
      "title": "export_HybridFinder_results",
      "topics": [
        "export_HybridFinder_results"
      ]
    },
    {
      "page": "export_step2_results",
      "title": "export_step2_results",
      "topics": [
        "export_step2_results"
      ]
    },
    {
      "page": "HybridFinder",
      "title": "HybridFinder",
      "topics": [
        "HybridFinder"
      ]
    },
    {
      "page": "mhc_check",
      "title": "mhc_check",
      "topics": [
        "mhc_check"
      ]
    },
    {
      "page": "netmhcpan_list_alleles",
      "title": "netmhcpan_list_alleles",
      "topics": [
        "netmhcpan_list_alleles"
      ]
    },
    {
      "page": "step2_wo_netMHCpan",
      "title": "step2_wo_netMHCpan",
      "topics": [
        "step2_wo_netMHCpan"
      ]
    }
  ],
  "_rundeps": [
    "ade4",
    "codetools",
    "doParallel",
    "foreach",
    "iterators",
    "lattice",
    "MASS",
    "nlme",
    "pixmap",
    "Rcpp",
    "RcppArmadillo",
    "segmented",
    "seqinr",
    "sp"
  ],
  "_vignettes": [
    {
      "source": "RHybridFinder.Rmd",
      "filename": "RHybridFinder.html",
      "title": "RHybridFinder",
      "author": "Frederic Saab, Peter Kubiniok",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Loading the package",
        "Example data",
        "Step 1",
        "HybridFinder",
        "Description",
        "Loading data",
        "Run HybridFinder",
        "Output",
        "Ouput 1: HybridFinder Step1 output (HF_step1_output)",
        "Ouput 2: List of step1 candidate hybrid peptides",
        "Ouput 3: merged proteome",
        "Export",
        "Interim external step: Second database search using the merged proteome",
        "Step2",
        "checknetMHCpan",
        "Run checknetMHCpan",
        "Ouput 1: netMHCpan results in long format",
        "Ouput 2: netMHCpan results in wide format",
        "Ouput 3: Database search results updated",
        "step2_wo_netMHCpan",
        "Run step2_wo_netMHCpan",
        "Ouput 1: netMHCpan-ready input",
        "Ouput 2: Database search results updated",
        "References"
      ],
      "created": "2021-06-21 05:10:07",
      "modified": "2021-08-17 15:30:24",
      "commits": 2
    }
  ],
  "_score": 2,
  "_indexed": true,
  "_nocasepkg": "rhybridfinder",
  "_universes": [
    "cran"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.2.0",
      "date": "2026-10-06T11:29:21.000Z",
      "distro": "resolute",
      "commit": "3a89236619fc5f249a816ae80fd4ea35daf251df",
      "fileid": "https://r2.ropensci.org/53178f16160119dd6f8dc4e20c6dcad6de6b73f68c4999f85a4d608e5a640c87",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37456187478"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.2.0",
      "date": "2026-10-06T11:29:17.000Z",
      "distro": "resolute",
      "commit": "3a89236619fc5f249a816ae80fd4ea35daf251df",
      "fileid": "https://r2.ropensci.org/a7b873ab1f182713528ef41bc2758249dd1b8a8905ad014d9e482d54b05c232b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37456187478"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.2.0",
      "date": "2026-10-06T11:29:16.000Z",
      "commit": "3a89236619fc5f249a816ae80fd4ea35daf251df",
      "fileid": "https://r2.ropensci.org/ea034064d131eda0d541d795a65bf019927791353cfa2b24b9626982cb4d1f9c",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37456187478"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.2.0",
      "date": "2026-10-06T11:28:32.000Z",
      "commit": "3a89236619fc5f249a816ae80fd4ea35daf251df",
      "fileid": "https://r2.ropensci.org/bfe68a6d3139e10ba1fdd10de01c3f5369098883d9dc82e085349f20030a7e71",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37456187478"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.2.0",
      "date": "2026-10-06T11:28:35.000Z",
      "commit": "3a89236619fc5f249a816ae80fd4ea35daf251df",
      "fileid": "https://r2.ropensci.org/7ae831836271cca491f90cac373364ca4afa7d63eb98bba156b53ac31846fa11",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37456187478"
    }
  ]
}