N-Gram Analysis of Biological Sequences

aaprop | Normalized amino acids properties |

add_1grams | Add 1-grams |

as.data.frame.feature_test | Coerce feature_test object to a data frame |

binarize | Binarize |

biogram-package | biogram - analysis of biological sequences using n-grams |

calc_criterion | Calculate value of criterion |

calc_cs | Calculate Chi-squared-based measure |

calc_ed | Calculate encoding distance |

calc_ig | Calculate IG for single feature |

calc_kl | Calculate KL divergence of features |

calc_pi | Calculate partition index |

calc_si | Compute similarity index |

cluster_reg_exp | Clustering of sequences based on regular expression |

code_ngrams | Code n-grams |

construct_ngrams | Construct and filter n-grams |

count_multigrams | Detect and count multiple n-grams in sequences |

count_ngrams | Count n-grams in sequences |

count_specified | Count specified n-grams |

count_total | Count total number of n-grams |

create_encoding | Create encoding |

create_feature_target | Create feature according to given contingency matrix |

create_ngrams | Get all possible n-Grams |

criterion_distribution | criterion_distribution class |

cut.feature_test | Categorize tested features |

decode_ngrams | Decode n-grams |

degenerate | Degenerate protein sequence |

distr_crit | Compute criterion distribution |

encoding2df | Convert encoding to data frame |

fast_crosstable | Very fast 2d cross-tabulation |

feature_test | feature_test class |

full2simple | Convert encoding from full to simple format |

gap_ngrams | Gap n-grams |

generate_sequence | Generate sequence |

generate_single_region | Generate single region |

generate_single_unigram | Generate single unigram |

generate_unigrams | Generate unigrams |

get_ngrams_ind | Get indices of n-grams |

human_cleave | Human signal peptides cleavage sites |

is_ngram | Validate n-gram |

l2n | Convert letters to numbers |

list2matrix | Convert list of sequences to matrix |

n2l | Convert numbers to letters |

ngrams2df | n-grams to data frame |

plot.criterion_distribution | Plot criterion distribution |

position_ngrams | Position n-grams |

print.feature_test | Print tested features |

regional_param | regional_param class |

seq2ngrams | Extract n-grams from sequence |

simple2full | Convert encoding from simple to full format |

simplify_alph | Simplify alphabets |

summary.feature_test | Summarize tested features |

table_ngrams | Tabulate n-grams |

test_features | Permutation test for feature selection |

validate_encoding | Validate encoding |

write_encoding | Write encodings to a file |

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