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  "Title": "DiffLogo: A comparative visualisation of biooligomer motifs",
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  "Date": "2015-02-12",
  "Author": "c( person(\"Martin\", \"Nettling\", role = c(\"aut\", \"cre\"), email =\n\"martin.nettling@informatik.uni-halle.de\"), person(\"Hendrik\",\n\"Treutler\", role = c(\"aut\", \"cre\"), email =\n\"hendrik.treutler@ipb-halle.de\"), person(\"Jan\", \"Grau\", role =\nc(\"aut\", \"ctb\"), email = \"grau@informatik.uni-halle.de\"),\nperson(\"Andrey\", \"Lando\", role = c(\"aut\", \"ctb\"), email =\n\"dronte@autosome.ru\"), person(\"Jens\", \"Keilwagen\", role =\nc(\"aut\", \"ctb\"), email = \"jens.keilwagen@julius-kuehn.de\"),\nperson(\"Stefan\", \"Posch\", role = \"aut\", email =\n\"posch@informatik.uni-halle.de\"), person(\"Ivo\", \"Grosse\", role\n= \"aut\", email = \"grosse@informatik.uni-halle.de\"))",
  "Maintainer": "Hendrik Treutler<hendrik.treutler@gmail.com>",
  "Description": "DiffLogo is an easy-to-use tool to visualize motif\ndifferences.",
  "License": "GPL (>= 2)",
  "URL": "https://github.com/mgledi/DiffLogo/",
  "BugReports": "https://github.com/mgledi/DiffLogo/issues",
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  "_realowner": "bioc",
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    "ASN",
    "calculatePvalue",
    "createDiffLogoObject",
    "differenceOfICs",
    "diffLogo",
    "diffLogoFromPwm",
    "diffLogoTable",
    "diffLogoTableConfiguration",
    "DNA",
    "drawDiffLogoTable",
    "enrichDiffLogoObjectWithPvalues",
    "enrichDiffLogoTableWithPvalues",
    "extendPwmsFromAlignmentVector",
    "FULL_ALPHABET",
    "getAlphabetFromCharacters",
    "getAlphabetFromSequences",
    "getPwmFromAlignment",
    "getPwmFromAlignmentFile",
    "getPwmFromFastaFile",
    "getPwmFromFile",
    "getPwmFromHomerFile",
    "getPwmFromPfmOrJasparFile",
    "getPwmFromPwmFile",
    "getSequencesFromAlignmentFile",
    "getSequencesFromFastaFile",
    "informationContent",
    "lossOfAbsICDifferences",
    "multipleLocalPwmsAlignment",
    "normalizedDifferenceOfProbabilities",
    "normalizePWM",
    "prepareDiffLogoTable",
    "probabilities",
    "pwmDivergence",
    "RNA",
    "seqLogo",
    "shannonDivergence",
    "sumOfAbsICDifferences",
    "sumOfAbsProbabilityDifferences",
    "sumProbabilities"
  ],
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    {
      "page": "alignPwmSets",
      "title": "Multiple PWMs alignment",
      "topics": [
        "alignPwmSets"
      ]
    },
    {
      "page": "Alphabet",
      "title": "built alphabet",
      "topics": [
        "Alphabet"
      ]
    },
    {
      "page": "ASN",
      "title": "ASN alphabet",
      "topics": [
        "ASN"
      ]
    },
    {
      "page": "baseDistributionPwm",
      "title": "Generates a PWM",
      "topics": [
        "baseDistributionPwm"
      ]
    },
    {
      "page": "calculatePvalue",
      "title": "p-value that two PWM-positions are from the same distribution",
      "topics": [
        "calculatePvalue"
      ]
    },
    {
      "page": "createDiffLogoObject",
      "title": "DiffLogo object",
      "topics": [
        "createDiffLogoObject"
      ]
    },
    {
      "page": "differenceOfICs",
      "title": "normalized information content differences",
      "topics": [
        "differenceOfICs"
      ]
    },
    {
      "page": "diffLogo",
      "title": "Draw DiffLogo",
      "topics": [
        "diffLogo"
      ]
    },
    {
      "page": "diffLogoFromPwm",
      "title": "Draw DiffLogo from PWM",
      "topics": [
        "diffLogoFromPwm"
      ]
    },
    {
      "page": "diffLogoTable",
      "title": "Draw DiffLogo-table",
      "topics": [
        "diffLogoTable"
      ]
    },
    {
      "page": "diffLogoTableConfiguration",
      "title": "Configuration object for diffLogoTable",
      "topics": [
        "diffLogoTableConfiguration"
      ]
    },
    {
      "page": "DNA",
      "title": "DNA alphabet",
      "topics": [
        "DNA"
      ]
    },
    {
      "page": "drawDiffLogoTable",
      "title": "Draws a table of DiffLogos",
      "topics": [
        "drawDiffLogoTable"
      ]
    },
    {
      "page": "enrichDiffLogoObjectWithPvalues",
      "title": "Enriches a difflogo object with p-values",
      "topics": [
        "enrichDiffLogoObjectWithPvalues"
      ]
    },
    {
      "page": "enrichDiffLogoTableWithPvalues",
      "title": "Enriches a matrix of difflogo objects with p-values",
      "topics": [
        "enrichDiffLogoTableWithPvalues"
      ]
    },
    {
      "page": "extendPwmsFromAlignmentVector",
      "title": "Extend pwms with respect to alignment",
      "topics": [
        "extendPwmsFromAlignmentVector"
      ]
    },
    {
      "page": "FULL_ALPHABET",
      "title": "Complete character alphabet",
      "topics": [
        "FULL_ALPHABET"
      ]
    },
    {
      "page": "getAlphabetFromCharacters",
      "title": "returns the alphabet which fits to the given characters",
      "topics": [
        "getAlphabetFromCharacters"
      ]
    },
    {
      "page": "getAlphabetFromSequences",
      "title": "returns the alphabet which fits to the given sequences",
      "topics": [
        "getAlphabetFromSequences"
      ]
    },
    {
      "page": "getPwmFromAlignment",
      "title": "Create PWM from alignment",
      "topics": [
        "getPwmFromAlignment"
      ]
    },
    {
      "page": "getPwmFromAlignmentFile",
      "title": "generates a pwm from an alignment file",
      "topics": [
        "getPwmFromAlignmentFile"
      ]
    },
    {
      "page": "getPwmFromFastaFile",
      "title": "generates a pwm from a FASTA file",
      "topics": [
        "getPwmFromFastaFile"
      ]
    },
    {
      "page": "getPwmFromFile",
      "title": "generates a pwm from a file of different formats",
      "topics": [
        "getPwmFromFile"
      ]
    },
    {
      "page": "getPwmFromHomerFile",
      "title": "generates a pwm from a homer file",
      "topics": [
        "getPwmFromHomerFile"
      ]
    },
    {
      "page": "getPwmFromPfmOrJasparFile",
      "title": "generates a pwm from a jaspar file",
      "topics": [
        "getPwmFromPfmOrJasparFile"
      ]
    },
    {
      "page": "getPwmFromPwmFile",
      "title": "generates a pwm from a pwm file",
      "topics": [
        "getPwmFromPwmFile"
      ]
    },
    {
      "page": "getSequencesFromAlignmentFile",
      "title": "extracts the sequences from an alignment file",
      "topics": [
        "getSequencesFromAlignmentFile"
      ]
    },
    {
      "page": "getSequencesFromFastaFile",
      "title": "extracts the sequences from a FASTA file",
      "topics": [
        "getSequencesFromFastaFile"
      ]
    },
    {
      "page": "informationContent",
      "title": "information content",
      "topics": [
        "informationContent"
      ]
    },
    {
      "page": "localPwmAlignment",
      "title": "Align pwms",
      "topics": [
        "localPwmAlignment"
      ]
    },
    {
      "page": "lossOfAbsICDifferences",
      "title": "the change of information content",
      "topics": [
        "lossOfAbsICDifferences"
      ]
    },
    {
      "page": "multipleLocalPwmsAlignment",
      "title": "Multiple PWMs alignment",
      "topics": [
        "multipleLocalPwmsAlignment"
      ]
    },
    {
      "page": "normalizedDifferenceOfProbabilities",
      "title": "normalized probability differences",
      "topics": [
        "normalizedDifferenceOfProbabilities"
      ]
    },
    {
      "page": "normalizePWM",
      "title": "normalizes the given pwm",
      "topics": [
        "normalizePWM"
      ]
    },
    {
      "page": "prepareDiffLogoTable",
      "title": "Prepare a table of difflogo objects",
      "topics": [
        "prepareDiffLogoTable"
      ]
    },
    {
      "page": "probabilities",
      "title": "probabilities",
      "topics": [
        "probabilities"
      ]
    },
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      "page": "pwmDivergence",
      "title": "PWM divergence",
      "topics": [
        "pwmDivergence"
      ]
    },
    {
      "page": "pwmsDistanceMatrix",
      "title": "Multiple PWMs alignment",
      "topics": [
        "pwmsDistanceMatrix"
      ]
    },
    {
      "page": "reverseAlignmentVector",
      "title": "Reverse for alignment vector",
      "topics": [
        "reverseAlignmentVector"
      ]
    },
    {
      "page": "RNA",
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      "topics": [
        "RNA"
      ]
    },
    {
      "page": "seqLogo",
      "title": "Draw sequence logo",
      "topics": [
        "seqLogo"
      ]
    },
    {
      "page": "shannonDivergence",
      "title": "shannon divergence",
      "topics": [
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      ]
    },
    {
      "page": "sumOfAbsICDifferences",
      "title": "sum of absolute information content differences",
      "topics": [
        "sumOfAbsICDifferences"
      ]
    },
    {
      "page": "sumOfAbsProbabilityDifferences",
      "title": "sum of absolute probability differences",
      "topics": [
        "sumOfAbsProbabilityDifferences"
      ]
    },
    {
      "page": "sumProbabilities",
      "title": "sum of probabilities, i.e. 1.0",
      "topics": [
        "sumProbabilities"
      ]
    },
    {
      "page": "switchDirection",
      "title": "Switches between 'forward' and 'reverse'",
      "topics": [
        "switchDirection"
      ]
    },
    {
      "page": "twoSetsAveragePwmDivergenceFromAlignmentVector",
      "title": "Average divergence between two sets.",
      "topics": [
        "twoSetsAveragePwmDivergenceFromAlignmentVector"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/DiffLogo/raw/HEAD/README.md",
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      "status": "success",
      "check": "WARNING",
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    }
  ]
}