{
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  "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": "2026-05-14 06:52:20 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",
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  "_type": "src",
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  "_commit": {
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    "author": "Frederic Saab <frederic.saab@umontreal.ca>",
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    "message": "version 0.2.0\n",
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    "name": "Frederic Saab",
    "email": "frederic.saab@umontreal.ca"
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    {
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    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
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      "role": "Suggests"
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  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
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  "_userbio": {
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    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RHybridFinder"
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/RHybridFinder.html",
    "manual.pdf"
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      "date": "2021-06-21"
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    "export_checknetmhcpan_results",
    "export_HybridFinder_results",
    "export_step2_results",
    "HybridFinder",
    "mhc_check",
    "step2_wo_netMHCpan"
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      "title": "db_Human_Liver_AUTD17",
      "object": "db_Human_Liver_AUTD17",
      "class": [
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      "fields": [
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        "X.10lgP",
        "Mass",
        "Length",
        "ppm",
        "m.z",
        "Z",
        "RT",
        "Area",
        "Fraction",
        "Id",
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      "object": "db_rerun_Human_Liver_AUTD17",
      "class": [
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        "RT",
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        "Fraction",
        "Id",
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        "AScore",
        "Found.By"
      ],
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      "title": "denovo_Human_Liver_AUTD17",
      "object": "denovo_Human_Liver_AUTD17",
      "class": [
        "data.frame"
      ],
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        "Source.File",
        "Feature",
        "Peptide",
        "Scan",
        "Tag.length",
        "Denovo.score",
        "ALC....",
        "Length",
        "m.z",
        "z",
        "RT",
        "Predict.RT",
        "Mass",
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        "local.confidence....",
        "tag....0..",
        "mode"
      ],
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      "table": true,
      "tojson": true
    }
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  "_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"
      ]
    }
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    "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
    }
  ],
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