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  "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",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:15 UTC",
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    "availableSchemes",
    "buildBackgroundModel",
    "cleanPeptides",
    "colorsets",
    "dagHeatmap",
    "dagLogo",
    "fetchSequence",
    "formatSequence",
    "getGroupingSymbol",
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    "prepareProteomeByFTP",
    "prepareProteomeByUniProtWS",
    "testDAU"
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      "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
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    {
      "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",
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      "topics": [
        "prepareProteomeByUniProtWS"
      ]
    },
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      "topics": [
        "Proteome",
        "Proteome-class"
      ]
    },
    {
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      "title": "An object of 'Proteome-class' representing the subset of _Drosophila melanogaster_ proteome.",
      "topics": [
        "proteome.example"
      ]
    },
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      "title": "An object of 'dagPeptides-class' representing acetylated lysine-containing peptides.",
      "topics": [
        "seq.example"
      ]
    },
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      "page": "testDAU",
      "title": "Differential usage test of amino acids or amino acid groups.",
      "topics": [
        "testDAU"
      ]
    },
    {
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      "title": "Class 'testDAUresults'.",
      "topics": [
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        "testDAUresults-class"
      ]
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        "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"
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      "created": "2015-09-24 16:33:30",
      "modified": "2020-08-27 17:25:00",
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