{
  "_id": "6a17e401acfb0bcc41da06e6",
  "Package": "dagLogo",
  "Type": "Package",
  "Title": "dagLogo: a Bioconductor package for visualizing conserved amino\nacid sequence pattern in groups based on probability theory",
  "Version": "1.51.0",
  "Author": "Jianhong Ou, Haibo Liu, Alexey Stukalov, Niraj Nirala, Usha\nAcharya, Lihua Julie Zhu",
  "Maintainer": "Jianhong Ou <jou@morgridge.org>",
  "Description": "Visualize significant conserved amino acid sequence\npattern in groups based on probability theory.",
  "License": "GPL (>=2)",
  "biocViews": "SequenceMatching, Visualization",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.2.1",
  "Encoding": "UTF-8",
  "LazyLoad": "yes",
  "LazyData": "true",
  "Config/pak/sysreqs": "cmake make libgsl0-dev libbz2-dev libicu-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:15 UTC",
  "RemoteUrl": "https://github.com/bioc/dagLogo",
  "RemoteRef": "HEAD",
  "RemoteSha": "20ded966c250272cfab483fbed64c3d5b9b67dd7",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 06:29:09 UTC",
    "User": "root"
  },
  "MD5sum": "f2199840056b5e9829dc0f35780318dd",
  "_user": "bioc",
  "_type": "src",
  "_file": "dagLogo_1.51.0.tar.gz",
  "_fileid": "7987bc72b95271be34b5ceb72c11dd40990a652f0ba0c03bd3c61120d0ad70a1",
  "_filesize": 2727773,
  "_sha256": "7987bc72b95271be34b5ceb72c11dd40990a652f0ba0c03bd3c61120d0ad70a1",
  "_created": "2026-05-28T06:29:09.000Z",
  "_published": "2026-05-28T06:43:13.543Z",
  "_jobs": [
    {
      "job": 78236279363,
      "time": 198,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7259204949"
    },
    {
      "job": 78236279442,
      "time": 490,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7259277949"
    },
    {
      "job": 78236279419,
      "time": 476,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259274176"
    },
    {
      "job": 78236279452,
      "time": 257,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7259345704"
    },
    {
      "job": 78236279401,
      "time": 311,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259333509"
    },
    {
      "job": 78235611668,
      "time": 341,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259153833"
    },
    {
      "job": 78236279501,
      "time": 185,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259201156"
    },
    {
      "job": 78236279417,
      "time": 360,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7259246373"
    },
    {
      "job": 78236279430,
      "time": 407,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7259257819"
    },
    {
      "job": 78236279447,
      "time": 375,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259250613"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 3,
    "note": 17
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26558490656",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/dagLogo",
  "_commit": {
    "id": "20ded966c250272cfab483fbed64c3d5b9b67dd7",
    "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": 1777379895
  },
  "_maintainer": {
    "name": "Jianhong Ou",
    "email": "jou@morgridge.org"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.1",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "grid",
      "role": "Depends"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "UniProt.ws",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "biomaRt",
      "role": "Imports"
    },
    {
      "package": "motifStack",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "XML",
      "role": "Suggests"
    },
    {
      "package": "grImport",
      "role": "Suggests"
    },
    {
      "package": "grImport2",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.51.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.50.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "sequencematching",
    "visualization"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 474,
    "source": "https://www.bioconductor.org/packages/stats/bioc/dagLogo"
  },
  "_mentions": 2,
  "_searchresults": 12,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/dagLogo.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/jianhong/daglogo",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addScheme",
    "availableSchemes",
    "buildBackgroundModel",
    "cleanPeptides",
    "colorsets",
    "dagHeatmap",
    "dagLogo",
    "fetchSequence",
    "formatSequence",
    "getGroupingSymbol",
    "prepareProteome",
    "prepareProteomeByFTP",
    "prepareProteomeByUniProtWS",
    "testDAU"
  ],
  "_datasets": [
    {
      "name": "ecoli.proteome",
      "title": "An object of 'Proteome-class' representing the _Escherichia coli_ proteome.",
      "object": "ecoli.proteome",
      "class": [
        "Proteome"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "proteome.example",
      "title": "An object of 'Proteome-class' representing the subset of _Drosophila melanogaster_ proteome.",
      "object": "proteome.example",
      "class": [
        "Proteome"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "seq.example",
      "title": "An object of 'dagPeptides-class' representing acetylated lysine-containing peptides.",
      "object": "seq.example",
      "class": [
        "dagPeptides"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "addScheme",
      "title": "Add a custom coloring or grouping scheme.",
      "topics": [
        "addScheme"
      ]
    },
    {
      "page": "availableSchemes",
      "title": "Get all predefined coloring and grouping schemes",
      "topics": [
        "availableSchemes"
      ]
    },
    {
      "page": "buildBackgroundModel",
      "title": "Build background models for DAU tests",
      "topics": [
        "buildBackgroundModel"
      ]
    },
    {
      "page": "cleanPeptides",
      "title": "clean up peptides",
      "topics": [
        "cleanPeptides"
      ]
    },
    {
      "page": "colorsets2",
      "title": "retrieve color setting for logo visualization",
      "topics": [
        "colorsets2"
      ]
    },
    {
      "page": "dagBackground-class",
      "title": "Class 'dagBackground'.",
      "topics": [
        "dagBackground",
        "dagBackground-class"
      ]
    },
    {
      "page": "dagHeatmap",
      "title": "Visualize daglogo using a heatmap.",
      "topics": [
        "dagHeatmap"
      ]
    },
    {
      "page": "dagLogo",
      "title": "Create sequence logo.",
      "topics": [
        "dagLogo"
      ]
    },
    {
      "page": "dagPeptides-class",
      "title": "Class 'dagPeptides'. An S4 class to represent formatted, aligned peptides for dagLogo analysis.",
      "topics": [
        "dagPeptides",
        "dagPeptides-class"
      ]
    },
    {
      "page": "ecoli.proteome",
      "title": "An object of 'Proteome-class' representing the _Escherichia coli_ proteome.",
      "topics": [
        "ecoli.proteome"
      ]
    },
    {
      "page": "fetchSequence",
      "title": "Fetch protein/peptide sequences and create a 'dagPeptides-class' object.",
      "topics": [
        "fetchSequence"
      ]
    },
    {
      "page": "formatSequence",
      "title": "Format already aligned peptide sequences.",
      "topics": [
        "formatSequence"
      ]
    },
    {
      "page": "nameHash",
      "title": "convert group name to a single character",
      "topics": [
        "nameHash"
      ]
    },
    {
      "page": "prepareProteome",
      "title": "prepare proteome for background building",
      "topics": [
        "prepareProteome"
      ]
    },
    {
      "page": "prepareProteomeByFTP",
      "title": "Create an object of 'Proteome' Class.",
      "topics": [
        "prepareProteomeByFTP"
      ]
    },
    {
      "page": "prepareProteomeByUniProtWS",
      "title": "Prepare a Proteome object for background building",
      "topics": [
        "prepareProteomeByUniProtWS"
      ]
    },
    {
      "page": "Proteome-class",
      "title": "Class 'Proteome'.",
      "topics": [
        "Proteome",
        "Proteome-class"
      ]
    },
    {
      "page": "proteome.example",
      "title": "An object of 'Proteome-class' representing the subset of _Drosophila melanogaster_ proteome.",
      "topics": [
        "proteome.example"
      ]
    },
    {
      "page": "seq.example",
      "title": "An object of 'dagPeptides-class' representing acetylated lysine-containing peptides.",
      "topics": [
        "seq.example"
      ]
    },
    {
      "page": "testDAU",
      "title": "Differential usage test of amino acids or amino acid groups.",
      "topics": [
        "testDAU"
      ]
    },
    {
      "page": "testDAUresults-class",
      "title": "Class 'testDAUresults'.",
      "topics": [
        "testDAUresults",
        "testDAUresults-class"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/dagLogo/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "ade4",
    "AnnotationDbi",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "bslib",
    "cachem",
    "caTools",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "digest",
    "DirichletMultinomial",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "gtools",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "motifStack",
    "openssl",
    "pheatmap",
    "pillar",
    "pixmap",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "pwalign",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rjsoncons",
    "rlang",
    "rmarkdown",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "seqLogo",
    "snow",
    "sp",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "TFBSTools",
    "TFMPvalue",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "UniProt.ws",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "dagLogo.Rmd",
      "filename": "dagLogo.html",
      "title": "dagLogo Vignette",
      "author": "Jianhong Ou, Haibo Liu, Lihua Julie Zhu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Step-by-step guide on using dagLogo",
        "First load the library dagLogo",
        "Step 1: Fetching peptide sequences from BioMart",
        "Case 1: Fetch sequences using the fetchSequence function in biomaRt package given a list of gene identifiers and the corresponding positions of the anchoring AA.",
        "Case 2: Fetch sequences using the fetchSequence function in biomaRt package given a list of gene identifiers and the corresponding peptide subsequences of interest with the anchoring AA marked such as asterisks or lower case of one or more AA letters.",
        "Case 3: Prepare an object of dagPeptides using prepareProteome and formatSequence functions sequentially given a list of unaligned/aligned ungapped peptide sequences.",
        "Step 2: Building background models",
        "Step 3: Statistical significance test for differential usage of amino acids with or without grouping",
        "Step 4: Visualize significance test results",
        "Session Info"
      ],
      "created": "2015-09-24 16:33:30",
      "modified": "2020-08-27 17:25:00",
      "commits": 16
    }
  ],
  "_score": 4.380211241711606,
  "_indexed": true,
  "_nocasepkg": "daglogo",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.51.0",
      "date": "2026-05-28T06:33:49.000Z",
      "distro": "noble",
      "commit": "20ded966c250272cfab483fbed64c3d5b9b67dd7",
      "fileid": "ff29598e06eff9ad47050f65aea253467f08d953d061443e5a5cd5b80dbda2b8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558490656"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.51.0",
      "date": "2026-05-28T06:33:37.000Z",
      "distro": "noble",
      "commit": "20ded966c250272cfab483fbed64c3d5b9b67dd7",
      "fileid": "8501e46dbaf24ebb5fcf47a6a132a1adabd92c67df0a8ce2c59e26399ffff49c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558490656"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.51.0",
      "date": "2026-05-28T06:40:03.000Z",
      "commit": "20ded966c250272cfab483fbed64c3d5b9b67dd7",
      "fileid": "1fb9b172045cd491b65d51d25ebd85c36777146d9f8255b905f08dae0ac34df8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558490656"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.51.0",
      "date": "2026-05-28T06:38:21.000Z",
      "commit": "20ded966c250272cfab483fbed64c3d5b9b67dd7",
      "fileid": "1626471a5e3e81414357012495cd074df8735909f18f8396f65d8f8bfaa68104",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558490656"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.51.0",
      "date": "2026-05-28T06:33:00.000Z",
      "commit": "20ded966c250272cfab483fbed64c3d5b9b67dd7",
      "fileid": "d6e910a44f9fda0807e7431f0ffb86b6a354bd44584f9bc9c0ad77744502343e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558490656"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-05-28T06:31:39.000Z",
      "commit": "20ded966c250272cfab483fbed64c3d5b9b67dd7",
      "fileid": "f2dba17592049fe1d883b0d1a68a0337f7bd48ca3ee1719be770ba318c7f21e9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558490656"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-05-28T06:31:45.000Z",
      "commit": "20ded966c250272cfab483fbed64c3d5b9b67dd7",
      "fileid": "cebcc312bb561cc9f29c4d33fb1e4061726c0a218509ddbc5d7339c2931d1e50",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558490656"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-05-28T06:31:37.000Z",
      "commit": "20ded966c250272cfab483fbed64c3d5b9b67dd7",
      "fileid": "dd9f216c533285f8538534a42ea66f21cafa97c54f15bb682905f61c89ea92c1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558490656"
    }
  ]
}