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R package implementing the NBLAST neuron search algorithm, as an add-on for the NeuroAnatomy Toolbox (nat) R package.
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README.md

nat.nblast

natverse Release Version CRAN status Build Status Docs

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:

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 devtools to install the development version:

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

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