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  "Title": "DiffLogo: A comparative visualisation of biooligomer motifs",
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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",
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      "title": "probabilities",
      "topics": [
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      "title": "PWM divergence",
      "topics": [
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    {
      "page": "pwmsDistanceMatrix",
      "title": "Multiple PWMs alignment",
      "topics": [
        "pwmsDistanceMatrix"
      ]
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      "page": "reverseAlignmentVector",
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        "RNA"
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    {
      "page": "seqLogo",
      "title": "Draw sequence logo",
      "topics": [
        "seqLogo"
      ]
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      "page": "shannonDivergence",
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      "title": "sum of absolute information content differences",
      "topics": [
        "sumOfAbsICDifferences"
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    },
    {
      "page": "sumOfAbsProbabilityDifferences",
      "title": "sum of absolute probability differences",
      "topics": [
        "sumOfAbsProbabilityDifferences"
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      "page": "sumProbabilities",
      "title": "sum of probabilities, i.e. 1.0",
      "topics": [
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    },
    {
      "page": "switchDirection",
      "title": "Switches between 'forward' and 'reverse'",
      "topics": [
        "switchDirection"
      ]
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    {
      "page": "twoSetsAveragePwmDivergenceFromAlignmentVector",
      "title": "Average divergence between two sets.",
      "topics": [
        "twoSetsAveragePwmDivergenceFromAlignmentVector"
      ]
    }
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  "_readme": "https://github.com/bioc/DiffLogo/raw/HEAD/README.md",
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      "fileid": "https://r2.ropensci.org/cfb151be57846343dbf4965ff657caa1b3de15dfa46cb8f6d0d746f53fd2fa1e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37460755067"
    }
  ]
}