# kmer

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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

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

To download the development version from 
GitHub, first ensure a C/C++ compliler is available and the 
[devtools](https://github.com/r-lib/devtools) R package is installed. 
Linux users will generally have a compiler installed by default; 
however Windows users may need to download 
[Rtools](https://cran.r-project.org/bin/windows/Rtools/) and Mac 
OSX users will need [Xcode](https://developer.apple.com/xcode) 
(note that these are not R packages). 
To download and install devtools, run 

```R
install.packages("devtools")
``` 

The `kmer` package can then be installed and loaded by running

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

### Help

An overview of the package and its functions can be found by running
```R
?kmer
```

To view the tutorial, you can either run
```R
vignette("kmer-vignette")
```
or access it directly from [CRAN](https://CRAN.R-project.org/package=kmer).

If you experience a problem using this package please feel free to
raise it as an issue on [GitHub](https://github.com/shaunpwilkinson/kmer/issues).
Any feedback is appreciated.

### Acknowledgements

This software was developed at 
[Victoria University of Wellington](https://www.wgtn.ac.nz/) 
with funding from a Rutherford Foundation Postdoctoral Research Fellowship 
award from the Royal Society of New Zealand.
