N-Gram Analysis of Biological Sequences

Tools for extraction and analysis of various n-grams (k-mers) derived from biological sequences (proteins or nucleic acids). Contains QuiPT (quick permutation test) for fast feature-filtering of the n-gram data.


This package contains 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 curse of dimensionality of the n-grams, biogram uses Quick Permutation Test (QuiPT) for fast feature filtering.

biogram is available on CRAN, so installation is as simple as:

install.packages("biogram")

You can install the latest development version of the code using the devtools R package.

install.packages("devtools")
 
library(devtools)
install_github("michbur/biogram")

For citation type:

citation("biogram")

or use: Michal Burdukiewicz, Piotr Sobczyk and Chris Lauber (2015). biogram: N-Gram Analysis of Biological Sequences. R package version 1.2. http://CRAN.R-project.org/package=biogram

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Reference manual

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install.packages("biogram")

1.4 by Michal Burdukiewicz, 9 months ago


https://github.com/michbur/biogram


Report a bug at https://github.com/michbur/biogram/issues


Browse source code at https://github.com/cran/biogram


Authors: Michal Burdukiewicz [cre, aut], Piotr Sobczyk [aut], Chris Lauber [aut]


Documentation:   PDF Manual  


GPL-3 license


Imports bit, combinat, entropy, partitions

Depends on slam

Suggests ggplot2, knitr, testthat


Imported by AmyloGram.


See at CRAN