nat.nblast is part of the NeuroAnatomy Toolbox suite of R packages.
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")
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:
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.
Use devtools to install the development version: