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  "Title": "N-Gram Analysis of Biological Sequences",
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  "Description": "Tools for extraction and analysis of various n-grams\n(k-mers) derived from biological sequences (proteins or nucleic\nacids). Contains QuiPT (quick permutation test) for fast\nfeature-filtering of the n-gram data. Compatibility updates by\nRenova.",
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  "Maintainer": "Michal Burdukiewicz <michalburdukiewicz@gmail.com>",
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    "calc_pi",
    "calc_si",
    "check_criterion",
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    "construct_ngrams",
    "count_multigrams",
    "count_ngrams",
    "count_specified",
    "count_total",
    "create_encoding",
    "create_feature_target",
    "create_ngrams",
    "decode_ngrams",
    "degenerate",
    "degenerate_ngrams",
    "distr_crit",
    "encoding2df",
    "fast_crosstable",
    "full2simple",
    "gap_ngrams",
    "generate_single_region",
    "generate_single_unigram",
    "generate_unigrams",
    "get_ngrams_ind",
    "is_ngram",
    "l2n",
    "list2matrix",
    "n2l",
    "ngrams2df",
    "position_ngrams",
    "read_fasta",
    "regenerate",
    "seq2ngrams",
    "simple2full",
    "table_ngrams",
    "test_features",
    "validate_encoding",
    "write_encoding",
    "write_fasta"
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      "object": "aaprop",
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        "array"
      ],
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        "r",
        "n",
        "d",
        "c",
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        "e",
        "g",
        "h",
        "i",
        "l",
        "k",
        "m",
        "f",
        "p",
        "s",
        "t",
        "w",
        "y",
        "v"
      ],
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      "table": true,
      "tojson": true
    },
    {
      "name": "human_cleave",
      "title": "Human signal peptides cleavage sites",
      "object": "human_cleave",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "P1",
        "P2",
        "P3",
        "P4",
        "P5",
        "P6",
        "P7",
        "P8",
        "P9",
        "tar"
      ],
      "rows": 1296,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "biogram-package",
      "title": "biogram - analysis of biological sequences using n-grams",
      "topics": [
        "biogram-package",
        "biogram"
      ]
    },
    {
      "page": "aaprop",
      "title": "Normalized amino acids properties",
      "topics": [
        "aaprop"
      ]
    },
    {
      "page": "add_1grams",
      "title": "Add 1-grams",
      "topics": [
        "add_1grams"
      ]
    },
    {
      "page": "as.data.frame.feature_test",
      "title": "Coerce feature_test object to a data frame",
      "topics": [
        "as.data.frame.feature_test"
      ]
    },
    {
      "page": "binarize",
      "title": "Binarize",
      "topics": [
        "binarize"
      ]
    },
    {
      "page": "calc_criterion",
      "title": "Calculate value of criterion",
      "topics": [
        "calc_criterion"
      ]
    },
    {
      "page": "calc_cs",
      "title": "Calculate Chi-squared-based measure",
      "topics": [
        "calc_cs"
      ]
    },
    {
      "page": "calc_ed",
      "title": "Calculate encoding distance",
      "topics": [
        "calc_ed"
      ]
    },
    {
      "page": "calc_ig",
      "title": "Calculate IG for single feature",
      "topics": [
        "calc_ig"
      ]
    },
    {
      "page": "calc_kl",
      "title": "Calculate KL divergence of features",
      "topics": [
        "calc_kl"
      ]
    },
    {
      "page": "calc_pi",
      "title": "Calculate partition index",
      "topics": [
        "calc_pi"
      ]
    },
    {
      "page": "calc_si",
      "title": "Compute similarity index",
      "topics": [
        "calc_si"
      ]
    },
    {
      "page": "check_criterion",
      "title": "Check chosen criterion",
      "topics": [
        "check_criterion"
      ]
    },
    {
      "page": "cluster_reg_exp",
      "title": "Clustering of sequences based on regular expression",
      "topics": [
        "cluster_reg_exp"
      ]
    },
    {
      "page": "code_ngrams",
      "title": "Code n-grams",
      "topics": [
        "code_ngrams"
      ]
    },
    {
      "page": "construct_ngrams",
      "title": "Construct and filter n-grams",
      "topics": [
        "construct_ngrams"
      ]
    },
    {
      "page": "count_multigrams",
      "title": "Detect and count multiple n-grams in sequences",
      "topics": [
        "count_multigrams"
      ]
    },
    {
      "page": "count_ngrams",
      "title": "Count n-grams in sequences",
      "topics": [
        "count_ngrams"
      ]
    },
    {
      "page": "count_specified",
      "title": "Count specified n-grams",
      "topics": [
        "count_specified"
      ]
    },
    {
      "page": "count_total",
      "title": "Count total number of n-grams",
      "topics": [
        "count_total"
      ]
    },
    {
      "page": "create_encoding",
      "title": "Create encoding",
      "topics": [
        "create_encoding"
      ]
    },
    {
      "page": "create_feature_target",
      "title": "Create feature according to given contingency matrix",
      "topics": [
        "create_feature_target"
      ]
    },
    {
      "page": "create_ngrams",
      "title": "Get all possible n-Grams",
      "topics": [
        "create_ngrams"
      ]
    },
    {
      "page": "criterion_distribution",
      "title": "criterion_distribution class",
      "topics": [
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      ]
    },
    {
      "page": "cut.feature_test",
      "title": "Categorize tested features",
      "topics": [
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      ]
    },
    {
      "page": "decode_ngrams",
      "title": "Decode n-grams",
      "topics": [
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      ]
    },
    {
      "page": "degenerate",
      "title": "Degenerate protein sequence",
      "topics": [
        "degenerate"
      ]
    },
    {
      "page": "degenerate_ngrams",
      "title": "Degenerate n-grams",
      "topics": [
        "degenerate_ngrams"
      ]
    },
    {
      "page": "distr_crit",
      "title": "Compute criterion distribution",
      "topics": [
        "distr_crit"
      ]
    },
    {
      "page": "encoding2df",
      "title": "Convert encoding to data frame",
      "topics": [
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      ]
    },
    {
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      "title": "2d cross-tabulation",
      "topics": [
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      ]
    },
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      "page": "feature_test",
      "title": "feature_test class",
      "topics": [
        "feature_test"
      ]
    },
    {
      "page": "full2simple",
      "title": "Convert encoding from full to simple format",
      "topics": [
        "full2simple"
      ]
    },
    {
      "page": "gap_ngrams",
      "title": "Gap n-grams",
      "topics": [
        "gap_ngrams"
      ]
    },
    {
      "page": "generate_sequence",
      "title": "Generate sequence",
      "topics": [
        "generate_sequence"
      ]
    },
    {
      "page": "generate_single_region",
      "title": "Generate single region",
      "topics": [
        "generate_single_region"
      ]
    },
    {
      "page": "generate_single_unigram",
      "title": "Generate single unigram",
      "topics": [
        "generate_single_unigram"
      ]
    },
    {
      "page": "generate_unigrams",
      "title": "Generate unigrams",
      "topics": [
        "generate_unigrams"
      ]
    },
    {
      "page": "get_ngrams_ind",
      "title": "Get indices of n-grams",
      "topics": [
        "get_ngrams_ind"
      ]
    },
    {
      "page": "human_cleave",
      "title": "Human signal peptides cleavage sites",
      "topics": [
        "human_cleave"
      ]
    },
    {
      "page": "is_ngram",
      "title": "Validate n-gram",
      "topics": [
        "is_ngram"
      ]
    },
    {
      "page": "l2n",
      "title": "Convert letters to numbers",
      "topics": [
        "l2n"
      ]
    },
    {
      "page": "list2matrix",
      "title": "Convert list of sequences to matrix",
      "topics": [
        "list2matrix"
      ]
    },
    {
      "page": "n2l",
      "title": "Convert numbers to letters",
      "topics": [
        "n2l"
      ]
    },
    {
      "page": "ngrams2df",
      "title": "n-grams to data frame",
      "topics": [
        "ngrams2df"
      ]
    },
    {
      "page": "plot.criterion_distribution",
      "title": "Plot criterion distribution",
      "topics": [
        "plot.criterion_distribution"
      ]
    },
    {
      "page": "position_ngrams",
      "title": "Position n-grams",
      "topics": [
        "position_ngrams"
      ]
    },
    {
      "page": "print.feature_test",
      "title": "Print tested features",
      "topics": [
        "print.feature_test"
      ]
    },
    {
      "page": "read_fasta",
      "title": "Read FASTA files",
      "topics": [
        "read_fasta"
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    },
    {
      "page": "regenerate",
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    {
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        "Reduction of dimensionality",
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        "Definition - entropy",
        "Definition -  conditional entropy",
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