Fast K-Mer Counting and Clustering for Biological Sequence Analysis

Contains tools for rapidly computing distance matrices and clustering large sequence datasets using fast alignment-free k-mer counting and recursive k-means partitioning. See Vinga and Almeida (2003) for a review of k-mer counting methods and applications for biological sequence analysis.



K-mer counting and clustering for biological sequence analysis

kmer is an R package for rapidly computing distance matrices and clustering large sequence datasets using fast alignment-free k-mer counting and recursive k-means partitioning.

Installation

To download kmer from CRAN and load the package, run

install.packages("kmer")
library("kmer")

To download the development version from GitHub, first ensure a C/C++ compliler is available and the devtools R package is installed. Linux users will generally have a compiler installed by default; however Windows users may need to download Rtools and Mac OSX users will need Xcode (note that these are not R packages). To download and install devtools, run

install.packages("devtools")

The kmer package can then be installed and loaded by running

devtools::install_github("shaunpwilkinson/kmer") 
library("kmer")

Help

An overview of the package and its functions can be found by running

?kmer

To view the tutorial, you can either run

vignette("kmer-vignette")

or access it directly from CRAN.

If you experience a problem using this package please feel free to raise it as an issue on GitHub. Any feedback is appreciated.

Acknowledgements

This software was developed at Victoria University of Wellington with funding from a Rutherford Foundation Postdoctoral Research Fellowship award from the Royal Society of New Zealand.

News

Reference manual

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install.packages("kmer")

1.1.0 by Shaun Wilkinson, 7 months ago


http://github.com/shaunpwilkinson/kmer


Report a bug at http://github.com/shaunpwilkinson/kmer/issues


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


Authors: Shaun Wilkinson [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Imports openssl, phylogram, Rcpp

Suggests ape, dendextend, knitr, rmarkdown, testthat

Linking to Rcpp


Imported by aphid, insect.


See at CRAN