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:
You can install the latest development version of the code using the
devtools R package.
For citation type:
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