NeuroAnatomy Toolbox ('nat') Extension for Assessing Neuron Similarity and Clustering

Extends package 'nat' (NeuroAnatomy Toolbox) by providing a collection of NBLAST-related functions for neuronal morphology comparison (Costa et al. (2016) ).

nat.nblast

nat.nblast is part of the NeuroAnatomy Toolbox suite of R packages.

Quick Start

For the impatient ...

# install
if (!require("devtools")) install.packages("devtools")
devtools::install_github(c("natverse/nat", "natverse/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

Costa M, Manton JD, Ostrovsky AD, Prohaska S, Jefferis GS. NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases.Neuron. 2016 Jul 20;91(2):293-311. doi: 10.1016/j.neuron.2016.06.012.

In addition to basic pairwise comparison, the package implements search of databases of neurons. There is also support 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 will be installed as dependency.

You will probably find the following online documentation helpful:

• https://natverse.org/nat.nblast/ - Online documentation for this R package
• https://jefferislab.org/si/nblast/ - Overview of NBLAST algorithm and online tools

Installation

This package has been released to CRAN (since v1.5), but we generally recommend installing the development version from GitHub, especially if you notice a bug.

CRAN release

install.packages("nat.nblast")

Development version

Use remotes to install the development version:

# install devtools if required
if (!require("remotes")) install.packages("remotes")
# then nat.nblast
remotes::install_github("natverse/nat.nblast")

Note that this will also update the nat package to the latest development version from github. Windows users need Rtools to install this way.