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biogram (version 1.0)

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

1.0

License

GPL-3

Issues

7

Pull Requests

0

Stars

10

Forks

1

Maintainer

Michal Burdukiewicz

Last Published

December 19th, 2014

Functions in biogram (1.0)

create_feature_target

Create feature according to given contingency matrix
data_sample

Subsample data
calc_ig

Calculate IG of features
criterion_distribution

Compute criterion distribution
count_multigrams

Detect and count multiple n-grams in sequences
fast_crosstable

Very fast 2d cross-tabulation
degenerate

Degenerate protein sequence
criterions

Critetions
seq2ngrams

Extract N-Grams From Sequence
human_cleave

Human signal peptides cleavage sites
create_ngrams

Get All Possible N-Grams
count_ngrams

Detect And Count N-Grams In Sequences
l2n

Convert letters to numbers
biogram-package

biogram - analysis of n-grams from biological sequences
prepare_data

Prepare data for further analysis
test_features

Permutation test for feature selection
get_ngrams_ind

Get Indices of N-Grams
calc_ig_single

Calculate IG for single feature
n2l

Convert numbers to letters