R: N-Gram Analysis of Biological Sequences

# N-Gram Analysis of Biological Sequences

## Documentation for package ‘biogram’ version 1.6.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

biogram-package | biogram - analysis of biological sequences using n-grams
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 | 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
check_criterion | Check chosen criterion
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
degenerate_ngrams | Degenerate n-grams
distr_crit | Compute criterion distribution
encoding2df | Convert encoding to data frame
fast_crosstable | 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
read_fasta | Read FASTA files
regenerate | Regenerate n-grams
regional_param | regional_param class
seq2ngrams | Extract n-grams from sequence
simple2full | Convert encoding from simple to full format
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
write_fasta | Write FASTA files