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

This package has now been released to CRAN (as of v1.5), but since this is the first official release, you may wish to install the development version from GitHub, especially if you notice a bug. Although nat (the main dependency) is available on CRAN, it it recommended that you install the development version of both packages if you want to install the development version of nat.nblast: nat.nblast is evolving fast and has required several minor tweaks to nat, which is otherwise quite mature.

CRAN release

install.packages("nat.nblast")

Development version

You can download the tar ball, and run R CMD INSTALL on it, or (recommended) use the devtools package to install the development version:

# 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.