# nat.nblast

## Quick Start

For the impatient ...

```
# install
if (!require("devtools")) install.packages("devtools")
devtools::install_github(c("jefferis/nat", "jefferislab/nat.nblast"))
# use
library(nat.nblast)
# run examples for search
example("nblast")
# run examples for clustering
example("nhclust")
# get overview help for package
?nat.nblast
# help for functions
?nblast
?nhclust
# run tests
library(testthat)
test_package("nat.nblast")
```

## Introduction

This R package implements the NBLAST neuron similarity algorithm described in a preprint available at `http://dx.doi.org/10.1101/006346`

. In addition to basic pairwise comparison, the package implements search of databases of neurons. There is also suport for all x all comparison for a group of neurons. This can produce a distance matrix suitable for hierarchical clustering, which is also implemented in the package.

These tools are designed as an addon for the NeuroAnatomy Toolbox (nat) R package, which you must first install.

## Installation

There is currently no released version of **nat.nblast** on CRAN. Although **nat** is available on CRAN, it it recommended that you install the development version of both packages from github; **nat.nblast** is evolving fast and has required several minor tweaks to **nat**, which is otherwise quite mature.

### Bleeding Edge

You can download the tar ball, and run `R CMD INSTALL`

on it, or (recommended) use the **devtools** package to install the development version:

`r # install devtools if required if (!require("devtools")) install.packages("devtools") # then install nat devtools::install_github("jefferis/nat") # then nat.nblast devtools::install_github("nat.nblast", "jefferislab")`

Note: Windows users need Rtools to install this way.