https://github.com/natverse/nat.nblast
R package implementing the NBLAST neuron search algorithm, as an add-on for the NeuroAnatomy Toolbox (nat) R package.
https://github.com/natverse/nat.nblast
morphological-analysis nblast neuroanatomy neuroanatomy-toolbox neurons
Last synced: 5 months ago
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R package implementing the NBLAST neuron search algorithm, as an add-on for the NeuroAnatomy Toolbox (nat) R package.
- Host: GitHub
- URL: https://github.com/natverse/nat.nblast
- Owner: natverse
- Created: 2014-04-22T10:54:53.000Z (about 12 years ago)
- Default Branch: master
- Last Pushed: 2025-08-18T11:32:59.000Z (10 months ago)
- Last Synced: 2025-08-18T13:25:46.722Z (10 months ago)
- Topics: morphological-analysis, nblast, neuroanatomy, neuroanatomy-toolbox, neurons
- Language: R
- Homepage: http://natverse.org/nat.nblast/
- Size: 6.55 MB
- Stars: 16
- Watchers: 4
- Forks: 6
- Open Issues: 17
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Support: .github/SUPPORT.md
Awesome Lists containing this project
README
# nat.nblast 
[](https://natverse.org/)
[](https://github.com/natverse/nat.nblast/releases/latest)
[](https://CRAN.R-project.org/package=nat.nblast)
[](https://natverse.org/nat.nblast/reference/)
[](https://github.com/natverse/nat.nblast/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/natverse/nat.nblast)
**nat.nblast** is part of the [NeuroAnatomy Toolbox](https://jefferislab.github.io/)
suite of R packages.
## Quick Start
For the impatient ...
```r
# 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](http://doi.org/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](https://natverse.org/nat/)
(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](https://cran.r-project.org/package=nat.nblast)
(since v1.5), but we generally recommend installing the development version from
GitHub, especially if you notice a bug.
### CRAN release
```r
install.packages("nat.nblast")
```
### Development version
Use **remotes** to install the development version:
```r
# 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](https://github.com/natverse/nat)
to the latest development version from github. Windows users need
[Rtools](https://cran.r-project.org/bin/windows/Rtools/) to install this way.