nat.nblast

Build Status

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.