{
  "_id": "6ad339c66814ce853b658740",
  "Package": "HERON",
  "Type": "Package",
  "Date": "2024-08-22",
  "Title": "Hierarchical Epitope pROtein biNding",
  "Version": "1.11.0",
  "Authors@R": "c(\nperson(given=\"Sean\",\nfamily = \"McIlwain\",\nrole = c(\"aut\", \"cre\"),\nemail = \"sean.mcilwain@wisc.edu\",\ncomment = c(ORCID=\"0000-0002-3820-8400\")),\nperson(given=\"Irene\",\nfamily = \"Ong\",\nrole = c(\"aut\"),\nemail = \"irene.ong@wisc.edu\",\ncomment = c(ORCID=\"0000-0002-9353-6941\"))\n)",
  "Description": "HERON is a software package for analyzing peptide binding\narray data. In addition to identifying significant binding\nprobes, HERON also provides functions for finding epitopes\n(string of consecutive peptides within a protein). HERON also\ncalculates significance on the probe, epitope, and protein\nlevel by employing meta p-value methods.  HERON is designed for\nobtaining calls on the sample level and calculates fractions of\nhits for different conditions.",
  "License": "GPL (>= 3)",
  "URL": "https://github.com/Ong-Research/HERON",
  "BugReports": "https://github.com/Ong-Research/HERON/issues",
  "Encoding": "UTF-8",
  "LazyData": "false",
  "RoxygenNote": "7.3.1",
  "biocViews": "Microarray, Software",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libabsl-dev cmake libfftw3-dev libgdal-dev gdal-bin\nlibgeos-dev libssl-dev libproj-dev libsqlite3-dev\nlibudunits2-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:16 UTC",
  "RemoteUrl": "https://github.com/bioc/HERON",
  "RemoteRef": "HEAD",
  "RemoteSha": "bef7869589fa5b8047dfb0daf5d89d9eab693580",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-17 08:46:09 UTC",
    "User": "root"
  },
  "Author": "Sean McIlwain [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3820-8400>),\nIrene Ong [aut] (ORCID: <https://orcid.org/0000-0002-9353-6941>)",
  "Maintainer": "Sean McIlwain <sean.mcilwain@wisc.edu>",
  "_user": "bioc",
  "_type": "src",
  "_file": "HERON_1.11.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/323fd18c7037425688131b47035ed2292426c6860b4e6b7b873050ffcf0e1615",
  "_filesize": 1130196,
  "_sha256": "323fd18c7037425688131b47035ed2292426c6860b4e6b7b873050ffcf0e1615",
  "_expires": "2027-01-25T09:03:00.000Z",
  "_created": "2026-10-17T08:46:09.000Z",
  "_published": "2026-10-17T09:03:02.041Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39018300425",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 2
  },
  "_upstream": "https://github.com/bioc/HERON",
  "_commit": {
    "id": "bef7869589fa5b8047dfb0daf5d89d9eab693580",
    "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": 1777381276
  },
  "_maintainer": {
    "name": "Sean McIlwain",
    "email": "sean.mcilwain@wisc.edu",
    "login": "mcilwain",
    "description": "",
    "uuid": 69368836,
    "orcid": "0000-0002-3820-8400"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 117355811286,
      "time": 169,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12096270322"
    },
    {
      "job": 117355811205,
      "time": 411,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12095049426"
    },
    {
      "job": 117355811271,
      "time": 424,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12095264096"
    },
    {
      "job": 117355811184,
      "time": 287,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12096227050"
    },
    {
      "job": 117355811196,
      "time": 244,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12096157353"
    },
    {
      "job": 117354890312,
      "time": 304,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12095349544"
    },
    {
      "job": 117355811204,
      "time": 130,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12096101105"
    },
    {
      "job": 117355811249,
      "time": 341,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12095428386"
    },
    {
      "job": 117355811252,
      "time": 295,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12095871666"
    },
    {
      "job": 117355811227,
      "time": 340,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12095692363"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "version": ">= 1.1.6",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "IRanges",
      "role": "Depends"
    },
    {
      "package": "S4Vectors",
      "role": "Depends"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "harmonicmeanp",
      "role": "Imports"
    },
    {
      "package": "metap",
      "role": "Imports"
    },
    {
      "package": "cluster",
      "role": "Imports"
    },
    {
      "package": "spdep",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.11.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.10.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "microarray",
    "software"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "mcilwain",
      "count": 171,
      "uuid": 69368836
    },
    {
      "user": "jwokaty",
      "count": 4,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 477,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 356,
    "source": "https://www.bioconductor.org/packages/stats/bioc/HERON"
  },
  "_devurl": "https://github.com/ong-research/heron",
  "_searchresults": 10,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/HERON.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/ong-research/heron",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    ".HERONEpitopeDataSet",
    ".HERONProbeDataSet",
    ".HERONProteinDataSet",
    ".HERONSequenceDataSet",
    "addSequenceAnnotations",
    "calcCombPValues",
    "calcEpitopePValues",
    "calcProbePValuesTPaired",
    "calcProbePValuesTUnpaired",
    "calcProbePValuesWUnpaired",
    "calcProteinPValues",
    "catSequences",
    "convertSequenceDSToProbeDS",
    "findBlocksProbeT",
    "findBlocksT",
    "findEpitopeSegments",
    "getEpitopeID",
    "getEpitopeIDsToProbeIDs",
    "getEpitopeProbeIDs",
    "getEpitopeProtein",
    "getEpitopeStart",
    "getEpitopeStop",
    "getKofN",
    "getProteinLabel",
    "getProteinStart",
    "getProteinTiling",
    "HERONEpitopeDataSet",
    "HERONProbeDataSet",
    "HERONProteinDataSet",
    "HERONSequenceDataSet",
    "log2Transform",
    "makeEpitopeCalls",
    "makeProbeCalls",
    "makeProteinCalls",
    "min_max",
    "oneHitEpitopes",
    "oneHitProbes",
    "oneProbeEpitopes",
    "pvalue_to_zscore",
    "quantileNormalize",
    "smoothProbeDS"
  ],
  "_datasets": [
    {
      "name": "heffron2021_wuhan",
      "title": "SARS CoV-2 Wuhan Peptide Binding Array Data",
      "object": "heffron2021_wuhan",
      "file": "heffron2021_wuhan.rda",
      "class": [
        "HERONSequenceDataSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "addSequenceAnnotations",
      "title": "Add Sequence Annotations for Epitopes",
      "topics": [
        "addSequenceAnnotations"
      ]
    },
    {
      "page": "calcCombPValues",
      "title": "Calculate p-values using the \"exprs\" assay",
      "topics": [
        "calcCombPValues"
      ]
    },
    {
      "page": "calcEpitopePValues",
      "title": "Calculate epitope-level p-values",
      "topics": [
        "calcEpitopePValues"
      ]
    },
    {
      "page": "calcProbePValuesTPaired",
      "title": "Calculate Probe p-values using a differential paired t-test",
      "topics": [
        "calcProbePValuesTPaired"
      ]
    },
    {
      "page": "calcProbePValuesTUnpaired",
      "title": "Calculate Probe p-values using a differential unpaired t-test",
      "topics": [
        "calcProbePValuesTUnpaired"
      ]
    },
    {
      "page": "calcProbePValuesWUnpaired",
      "title": "Calculate Probe p-values using a two-sample wilcoxon test",
      "topics": [
        "calcProbePValuesWUnpaired"
      ]
    },
    {
      "page": "calcProteinPValues",
      "title": "Calculate protein-level p-values",
      "topics": [
        "calcProteinPValues"
      ]
    },
    {
      "page": "catSequences",
      "title": "Concatenate sequences together based upon their start positions. Assumes the probe sequences have an overlap.",
      "topics": [
        "catSequences"
      ]
    },
    {
      "page": "convertSequenceDSToProbeDS",
      "title": "Convert HERONSequenceDataSet to HERONProbeDataSet",
      "topics": [
        "convertSequenceDSToProbeDS"
      ]
    },
    {
      "page": "findBlocksProbeT",
      "title": "Find Blocks of consecutive probes",
      "topics": [
        "findBlocksProbeT"
      ]
    },
    {
      "page": "findBlocksT",
      "title": "Find consecutive probes",
      "topics": [
        "findBlocksT"
      ]
    },
    {
      "page": "findEpitopeSegments",
      "title": "Find Epitopes from probe stats and calls.",
      "topics": [
        "findEpitopeSegments"
      ]
    },
    {
      "page": "getEpitopeID",
      "title": "Create EpitopeID from protein, first and last probes",
      "topics": [
        "getEpitopeID"
      ]
    },
    {
      "page": "getEpitopeIDsToProbeIDs",
      "title": "Get probe ids from a vector of epitope ids",
      "topics": [
        "getEpitopeIDsToProbeIDs"
      ]
    },
    {
      "page": "getEpitopeProbeIDs",
      "title": "Get the vector of probes from an epitope id",
      "topics": [
        "getEpitopeProbeIDs"
      ]
    },
    {
      "page": "getEpitopeProtein",
      "title": "Obtain Protein Id from Epitope ID",
      "topics": [
        "getEpitopeProtein"
      ]
    },
    {
      "page": "getEpitopeStart",
      "title": "Obtain first probe's protein start position from Epitope ID",
      "topics": [
        "getEpitopeStart"
      ]
    },
    {
      "page": "getEpitopeStop",
      "title": "Obtain last probe's protein start position from EpitopeID",
      "topics": [
        "getEpitopeStop"
      ]
    },
    {
      "page": "getKofN",
      "title": "Get K of N statistics from an experiment with padj and calls",
      "topics": [
        "getKofN"
      ]
    },
    {
      "page": "getProteinLabel",
      "title": "Get Protein Label from Probe",
      "topics": [
        "getProteinLabel"
      ]
    },
    {
      "page": "getProteinStart",
      "title": "Get the amino-acid starting position of the probe within the protein.",
      "topics": [
        "getProteinStart"
      ]
    },
    {
      "page": "getProteinTiling",
      "title": "Get Protein Tiling",
      "topics": [
        "getProteinTiling"
      ]
    },
    {
      "page": "heffron2021_wuhan",
      "title": "SARS CoV-2 Wuhan Peptide Binding Array Data",
      "topics": [
        "heffron2021_wuhan"
      ]
    },
    {
      "page": "HERONEpitopeDataSet",
      "title": "HERONEpitopeDataSet object and constructors",
      "topics": [
        ".HERONEpitopeDataSet",
        "HERONEpitopeDataSet",
        "HERONEpitopeDataSet-class"
      ]
    },
    {
      "page": "HERONProbeDataSet",
      "title": "HERONProbeDataSet object and constructors",
      "topics": [
        ".HERONProbeDataSet",
        "HERONProbeDataSet",
        "HERONProbeDataSet-class"
      ]
    },
    {
      "page": "HERONProteinDataSet",
      "title": "HERONProteinDataSet object and constructors",
      "topics": [
        ".HERONProteinDataSet",
        "HERONProteinDataSet",
        "HERONProteinDataSet-class"
      ]
    },
    {
      "page": "HERONSequenceDataSet",
      "title": "HERONSequenceDataSet object and constructors",
      "topics": [
        ".HERONSequenceDataSet",
        "HERONSequenceDataSet",
        "HERONSequenceDataSet-class"
      ]
    },
    {
      "page": "log2Transform",
      "title": "log2 transform the \"exprs\" assay",
      "topics": [
        "log2Transform"
      ]
    },
    {
      "page": "makeEpitopeCalls",
      "title": "Make Epitope Calls",
      "topics": [
        "makeEpitopeCalls"
      ]
    },
    {
      "page": "makeProbeCalls",
      "title": "Making Probe-level Calls",
      "topics": [
        "makeProbeCalls"
      ]
    },
    {
      "page": "makeProteinCalls",
      "title": "Make Protein-level Calls",
      "topics": [
        "makeProteinCalls"
      ]
    },
    {
      "page": "min_max",
      "title": "Cap vector at minimum/maximum values",
      "topics": [
        "min_max"
      ]
    },
    {
      "page": "oneHitEpitopes",
      "title": "Find One-hit epitopes",
      "topics": [
        "oneHitEpitopes"
      ]
    },
    {
      "page": "oneHitProbes",
      "title": "Find one hit probes",
      "topics": [
        "oneHitProbes"
      ]
    },
    {
      "page": "oneProbeEpitopes",
      "title": "Indicate which epitopes are just one probe.",
      "topics": [
        "oneProbeEpitopes"
      ]
    },
    {
      "page": "probeHitSupported",
      "title": "Find probe hits with a consecutive probe or another sample",
      "topics": [
        "probeHitSupported"
      ]
    },
    {
      "page": "pvalue_to_zscore",
      "title": "Convert p-value matrix to a z-score matrix",
      "topics": [
        "pvalue_to_zscore"
      ]
    },
    {
      "page": "quantileNormalize",
      "title": "Normalize the exprs assay using quantile normalization",
      "topics": [
        "quantileNormalize"
      ]
    },
    {
      "page": "smoothProbeDS",
      "title": "Smooth probes across protein tiling",
      "topics": [
        "smoothProbeDS"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/HERON/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "Biobase",
    "BiocGenerics",
    "boot",
    "class",
    "classInt",
    "cluster",
    "codetools",
    "data.table",
    "DBI",
    "DelayedArray",
    "deldir",
    "DEoptimR",
    "e1071",
    "FMStable",
    "generics",
    "GenomicRanges",
    "harmonicmeanp",
    "IRanges",
    "KernSmooth",
    "lattice",
    "limma",
    "MASS",
    "mathjaxr",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "metap",
    "mnormt",
    "multcomp",
    "multtest",
    "mutoss",
    "mvtnorm",
    "numDeriv",
    "plotrix",
    "proxy",
    "qqconf",
    "quantreg",
    "rbibutils",
    "Rcpp",
    "Rdpack",
    "robustbase",
    "s2",
    "S4Arrays",
    "S4Vectors",
    "sandwich",
    "Seqinfo",
    "sf",
    "sn",
    "sp",
    "SparseArray",
    "SparseM",
    "spData",
    "spdep",
    "statmod",
    "SummarizedExperiment",
    "survival",
    "TFisher",
    "TH.data",
    "units",
    "wk",
    "XVector",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "full_analysis.Rmd",
      "filename": "full_analysis.html",
      "title": "Analyzing High Density Peptide Array Data using HERON",
      "engine": "knitr::rmarkdown",
      "headings": [
        "HERON",
        "Installation",
        "Example",
        "The HERONSequenceData object",
        "Sequence matrix",
        "colData",
        "Probe metadata",
        "Creating the HERONSequenceData object",
        "Pre-process data",
        "Calculate probe-level p-values",
        "Obtain probe-level calls",
        "Find Epitope Segments using the unique method",
        "Calculate Epitope-level p-values",
        "Obtain Epitope-level calls",
        "Calculate Protein-level p-values",
        "Obtain Protein-level calls",
        "Other",
        "Find Epitope Segments using the hclust method",
        "binary calls with hamming distance",
        "z-scores with euclidean distance",
        "Find Epitope Segments using the skater method",
        "Other meta p-value methods",
        "Making z-score cutoff calls",
        "Smoothing across probes",
        "Calculate paired t-tests",
        "Use the wilcox test for probe-level p-values",
        "Use of the condition column",
        "Funding",
        "Acknowledgments",
        "Session Info"
      ],
      "created": "2022-10-11 14:29:47",
      "modified": "2024-08-22 20:09:24",
      "commits": 36
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "heron",
  "_universes": [
    "bioc",
    "mcilwain",
    "ong-research"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-10-17T08:49:25.000Z",
      "distro": "resolute",
      "commit": "bef7869589fa5b8047dfb0daf5d89d9eab693580",
      "fileid": "https://r2.ropensci.org/74c7df3a49fceca3e5d641a4b38779055229f78b096ba83a6ae0c3874f8ea614",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018300425"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-10-17T08:50:49.000Z",
      "distro": "resolute",
      "commit": "bef7869589fa5b8047dfb0daf5d89d9eab693580",
      "fileid": "https://r2.ropensci.org/8d80849f3577085d5f3036ab038b1cf32a8d8c7349538429faff2598f6d13cb4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018300425"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-10-17T08:59:05.000Z",
      "commit": "bef7869589fa5b8047dfb0daf5d89d9eab693580",
      "fileid": "https://r2.ropensci.org/d5ad267e2c869c1ed1cacd10ba113017e414257caa2bc428e0a6dab4ccd15b37",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018300425"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-10-17T08:59:57.000Z",
      "commit": "bef7869589fa5b8047dfb0daf5d89d9eab693580",
      "fileid": "https://r2.ropensci.org/08e44c031dc1c54869982a943a024b0fbe0eb72ac478ccf6903c69284294068b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018300425"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.11.0",
      "date": "2026-10-17T08:48:48.000Z",
      "commit": "bef7869589fa5b8047dfb0daf5d89d9eab693580",
      "fileid": "https://r2.ropensci.org/eac56bd525a1bee412ac1e2c966ba2c7d2820df75bbb441810389de3b98e8a5d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018300425"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-10-17T08:47:47.000Z",
      "commit": "bef7869589fa5b8047dfb0daf5d89d9eab693580",
      "fileid": "https://r2.ropensci.org/548929553e490cb656e4826b33724ad6d70fcac10f3a9224e38fc121be7928d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018300425"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-10-17T08:47:50.000Z",
      "commit": "bef7869589fa5b8047dfb0daf5d89d9eab693580",
      "fileid": "https://r2.ropensci.org/cbf8bf5ad3efeb93ca2314c813cd63b15093dc86eda004d73a307a730f1f5ef5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018300425"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-10-17T08:47:45.000Z",
      "commit": "bef7869589fa5b8047dfb0daf5d89d9eab693580",
      "fileid": "https://r2.ropensci.org/ef8450d4aec5ea8454acd5ac538d2f774cb701058eb40f72fc27532c4c4e38b6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018300425"
    }
  ]
}