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kmer

K-mer counting and clustering for biological sequence analysis

kmer is an R package for rapidly computing distancematrices and clustering large sequence datasets using fastalignment-free k-mer counting and recursive k-means partitioning.

Installation

To downloadkmer 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 thedevtools R package isinstalled. Linux users will generally have a compiler installed bydefault; however Windows users may need to downloadRtools and MacOSX users will needXcode (note that these arenot R packages). To download and install devtools, run

install.packages("devtools")

Thekmer package can then be installed and loaded byrunning

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

Help

An overview of the package and its functions can be found byrunning

?kmer

To view the tutorial, you can either run

vignette("kmer-vignette")

or access it directly fromCRAN.

If you experience a problem using this package please feel free toraise it as an issue onGitHub. Anyfeedback is appreciated.

Acknowledgements

This software was developed atVictoria University of Wellingtonwith funding from a Rutherford Foundation Postdoctoral ResearchFellowship award from the Royal Society of New Zealand.