Man pages for biogram
N-Gram Analysis of Biological Sequences

aapropNormalized amino acids properties
add_1gramsAdd 1-grams feature_test object to a data frame
biogram-packagebiogram - analysis of biological sequences using n-grams
calc_criterionCalculate value of criterion
calc_csCalculate Chi-squared-based measure
calc_edCalculate encoding distance
calc_igCalculate IG for single feature
calc_klCalculate KL divergence of features
calc_piCalculate partition index
calc_siCompute similarity index
check_criterionCheck chosen criterion
cluster_reg_expClustering of sequences based on regular expression
code_ngramsCode n-grams
construct_ngramsConstruct and filter n-grams
count_multigramsDetect and count multiple n-grams in sequences
count_ngramsCount n-grams in sequences
count_specifiedCount specified n-grams
count_totalCount total number of n-grams
create_encodingCreate encoding
create_feature_targetCreate feature according to given contingency matrix
create_ngramsGet all possible n-Grams
criterion_distributioncriterion_distribution class
cut.feature_testCategorize tested features
decode_ngramsDecode n-grams
degenerateDegenerate protein sequence
degenerate_ngramsDegenerate n-grams
distr_critCompute criterion distribution
encoding2dfConvert encoding to data frame
fast_crosstable2d cross-tabulation
feature_testfeature_test class
full2simpleConvert encoding from full to simple format
gap_ngramsGap n-grams
generate_sequenceGenerate sequence
generate_single_regionGenerate single region
generate_single_unigramGenerate single unigram
generate_unigramsGenerate unigrams
get_ngrams_indGet indices of n-grams
human_cleaveHuman signal peptides cleavage sites
is_ngramValidate n-gram
l2nConvert letters to numbers
list2matrixConvert list of sequences to matrix
n2lConvert numbers to letters
ngrams2dfn-grams to data frame
plot.criterion_distributionPlot criterion distribution
position_ngramsPosition n-grams
print.feature_testPrint tested features
read_fastaRead FASTA files
regenerateRegenerate n-grams
regional_paramregional_param class
seq2ngramsExtract n-grams from sequence
simple2fullConvert encoding from simple to full format
summary.feature_testSummarize tested features
table_ngramsTabulate n-grams
test_featuresPermutation test for feature selection
validate_encodingValidate encoding
write_encodingWrite encodings to a file
write_fastaWrite FASTA files
biogram documentation built on March 31, 2020, 5:14 p.m.