{
  "_id": "6a4943e418cdde069385ee31",
  "Package": "DominoEffect",
  "Type": "Package",
  "Title": "Identification and Annotation of Protein Hotspot Residues",
  "Version": "1.33.0",
  "Author": "Marija Buljan and Peter Blattmann",
  "Maintainer": "Marija Buljan <marija.buljan.2@gmail.com>, Peter Blattmann\n<peter_blattmann@bluewin.ch>",
  "Description": "The functions support identification and annotation of\nhotspot residues in proteins. These are individual amino acids\nthat accumulate mutations at a much higher rate than their\nsurrounding regions.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "6.0.1",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, SomaticMutation, Proteomics, SequenceMatching,\nAlignment",
  "NeedsCompilation": "no",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:19 UTC",
  "RemoteUrl": "https://github.com/bioc/DominoEffect",
  "RemoteRef": "HEAD",
  "RemoteSha": "cb54b0bac046a05e92795d293c1f1ffe3d9bb229",
  "Packaged": {
    "Date": "2026-07-04 13:51:31 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "DominoEffect_1.33.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/9e2ef9e914da36f1b551e075485604bf36af83d5868711691221d4d8f26e6ef8",
  "_filesize": 589001,
  "_sha256": "9e2ef9e914da36f1b551e075485604bf36af83d5868711691221d4d8f26e6ef8",
  "_expires": "2026-10-12T17:33:22.000Z",
  "_created": "2026-07-04T13:51:31.000Z",
  "_published": "2026-07-04T17:33:24.458Z",
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 10
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28708183713",
  "_status": "success",
  "_upstream": "https://github.com/bioc/DominoEffect",
  "_commit": {
    "id": "cb54b0bac046a05e92795d293c1f1ffe3d9bb229",
    "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": 1777380439
  },
  "_maintainer": {
    "name": "Marija Buljan",
    "email": "peter_blattmann@bluewin.ch",
    "login": "marijabuljan",
    "description": "",
    "uuid": 77449761
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85152582182,
      "time": 206,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8082303595"
    },
    {
      "job": 85152582272,
      "time": 576,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8082347246"
    },
    {
      "job": 85152582222,
      "time": 535,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8082342066"
    },
    {
      "job": 85152582332,
      "time": 326,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8082317205"
    },
    {
      "job": 85152582223,
      "time": 381,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8082323711"
    },
    {
      "job": 85152581930,
      "time": 328,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8082279535"
    },
    {
      "job": 85152582246,
      "time": 166,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8082298864"
    },
    {
      "job": 85152582089,
      "time": 415,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8082327653"
    },
    {
      "job": 85152582184,
      "time": 415,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8082327773"
    },
    {
      "job": 85152582345,
      "time": 369,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8082322432"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "biomaRt",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "pwalign",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "VariantAnnotation",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-30",
      "n": 2
    },
    {
      "week": "2025-40",
      "n": 2
    },
    {
      "week": "2025-41",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.33.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "somaticmutation",
    "proteomics",
    "sequencematching",
    "alignment"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 1,
  "_searchresults": 1,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DominoEffect.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "align_to_unip",
    "calculate_boundary",
    "DominoEffect",
    "GPo_of_hotspots",
    "identify_hotspots",
    "import_txdb",
    "map_to_func_elem"
  ],
  "_datasets": [
    {
      "name": "DominoData",
      "title": "Sample data",
      "object": "DominoData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Ensembl_gene_id",
        "Representative_tr",
        "cDNA_length",
        "Gene_name",
        "Uniprot_id"
      ],
      "rows": 20300,
      "table": true,
      "tojson": true
    },
    {
      "name": "SnpData",
      "title": "Sample data",
      "object": "SnpData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Chr_name",
        "Position_on_chr",
        "Minor_allele_freq"
      ],
      "rows": 423,
      "table": true,
      "tojson": true
    },
    {
      "name": "TestData",
      "title": "Sample data",
      "object": "TestData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Ensembl_gene_id",
        "Protein_residue",
        "Original_aa",
        "Mutated_aa",
        "Patient_id",
        "Genomic_coordinate",
        "Original_base",
        "Mutated_base"
      ],
      "rows": 1820,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "align_to_unip",
      "title": "Align protein segnent around the hotspot to the UniProt/Swiss-Prot KB sequence.",
      "topics": [
        "align_to_unip"
      ]
    },
    {
      "page": "calculate_boundary",
      "title": "calculate_boundary",
      "topics": [
        "calculate_boundary"
      ]
    },
    {
      "page": "data",
      "title": "Sample data",
      "topics": [
        "DominoData",
        "SnpData",
        "TestData"
      ]
    },
    {
      "page": "DominoEffect",
      "title": "Identification of significant mutation hotspot residues.",
      "topics": [
        "DominoEffect"
      ]
    },
    {
      "page": "GPo_of_hotspots",
      "title": "Converts hotspot mutation table into a GPo object",
      "topics": [
        "GPo_of_hotspots"
      ]
    },
    {
      "page": "identify_hotspots",
      "title": "Identify hotspots",
      "topics": [
        "identify_hotspots"
      ]
    },
    {
      "page": "import_txdb",
      "title": "Imports txdb data and converts it into format required for DominoEffect package",
      "topics": [
        "import_txdb"
      ]
    },
    {
      "page": "map_to_func_elem",
      "title": "Functional annotation of significant hotspot residues.",
      "topics": [
        "map_to_func_elem"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "glue",
    "hms",
    "httr",
    "httr2",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "pwalign",
    "R6",
    "rappdirs",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "withr",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "Vignette.Rmd",
      "filename": "Vignette.html",
      "title": "Vignette for DominoEffect package",
      "author": "Marija Buljan and Peter Blattmann",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Running the package",
        "Optional",
        "Description",
        "Set options",
        "Analysis",
        "MutationData, DominoData, and SnpData",
        "Convert results into GPo object",
        "Additional"
      ],
      "created": "2018-02-08 11:13:37",
      "modified": "2021-04-16 14:12:30",
      "commits": 7
    }
  ],
  "_score": 3.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "dominoeffect",
  "_universes": [
    "bioc",
    "marijabuljan"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-07-04T13:55:26.000Z",
      "distro": "resolute",
      "commit": "cb54b0bac046a05e92795d293c1f1ffe3d9bb229",
      "fileid": "https://r2.ropensci.org/17303fa66ee08aa8d4e5e199f6d3dabc960d56bd0820f59d02c09cf794b00c40",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708183713"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-07-04T13:55:50.000Z",
      "distro": "resolute",
      "commit": "cb54b0bac046a05e92795d293c1f1ffe3d9bb229",
      "fileid": "https://r2.ropensci.org/1df24dd57f50393ee7264f56754fb26df7f576ab208e29f6502fcaa287b5d5f0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708183713"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-07-04T13:53:37.000Z",
      "commit": "cb54b0bac046a05e92795d293c1f1ffe3d9bb229",
      "fileid": "https://r2.ropensci.org/6d8be8b5d5adea7b2572f57042d553d1cb032bd95fd42bb37bfaa23cde5c171b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708183713"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-07-04T13:53:55.000Z",
      "commit": "cb54b0bac046a05e92795d293c1f1ffe3d9bb229",
      "fileid": "https://r2.ropensci.org/0348cc92f9b510a3ac2f37b1d3b3a29df3424051dfb57f79634ce3ee44118a8d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708183713"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.33.0",
      "date": "2026-07-04T13:55:02.000Z",
      "commit": "cb54b0bac046a05e92795d293c1f1ffe3d9bb229",
      "fileid": "https://r2.ropensci.org/3fcc1cbb57be247a4f665ca5f2f3ef420bd222e3f54e5a0644e64a0616b6ef03",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708183713"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-04T13:53:38.000Z",
      "commit": "cb54b0bac046a05e92795d293c1f1ffe3d9bb229",
      "fileid": "https://r2.ropensci.org/a4ac06e32c4cef5a15bb787c13d1a1e8a8eeda2b12062924c1d984d9a97dbb66",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708183713"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-04T13:53:41.000Z",
      "commit": "cb54b0bac046a05e92795d293c1f1ffe3d9bb229",
      "fileid": "https://r2.ropensci.org/4d3b437fc3c64d9b27d5c4977b3a150368d6f4ec2249a2a45b8e604dc1f1606e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708183713"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-04T13:53:34.000Z",
      "commit": "cb54b0bac046a05e92795d293c1f1ffe3d9bb229",
      "fileid": "https://r2.ropensci.org/7f22444e42b0d388a8792a4807e17676fdf257866af6e26c20fbbc48986df81b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708183713"
    }
  ]
}