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biogram (version 1.1)

N-Gram Analysis of Biological Sequences

Description

Tools for extraction and analysis of various n-grams (sequences of n items) derived from biological sequences (proteins or nucleic acids). To deal with the dimensionality of the n-gram data, biogram uses QuiPT (quick permutation test) for fast feature-filtering.

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Version

Install

install.packages('biogram')

Monthly Downloads

259

Version

1.1

License

GPL-3

Issues

7

Pull Requests

0

Stars

10

Forks

1

Maintainer

Michal Burdukiewicz

Last Published

February 3rd, 2015

Functions in biogram (1.1)

cut.feature_test

Categorize tested features
biogram-package

biogram - analysis of biological sequences using n-grams
seq2ngrams

Extract N-Grams From Sequence
calc_ig_single

Calculate IG for single feature
fast_crosstable

Very fast 2d cross-tabulation
test_features

Permutation test for feature selection
feature_test

feature_test class
calc_ig

Calculate IG of features
criterions

Critetions
human_cleave

Human signal peptides cleavage sites
decode_ngrams

Decode n-grams
summary.feature_test

Summarize tested features
position_ngrams

Position n-grams
degenerate

Degenerate protein sequence
count_ngrams

Count n-grams in sequences
count_multigrams

Detect and count multiple n-grams in sequences
get_ngrams_ind

Get Indices of N-Grams
n2l

Convert numbers to letters
is_ngram

Validate n-gram
criterion_distribution

Compute criterion distribution
print.feature_test

Print tested features
l2n

Convert letters to numbers
create_feature_target

Create feature according to given contingency matrix
create_ngrams

Get All Possible N-Grams