Extends package 'nat' (NeuroAnatomy Toolbox) by providing a
collection of NBLAST-related functions for neuronal morphology comparison (Costa et al. (2016)
For the impatient ...
# installif (!require("devtools")) install.packages("devtools")devtools::install_github(c("jefferis/nat", "jefferislab/nat.nblast"))# uselibrary(nat.nblast)# run examples for searchexample("nblast")# run examples for clusteringexample("nhclust")# get overview help for package?nat.nblast# help for functions?nblast?nhclust# run testslibrary(testthat)test_package("nat.nblast")
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.
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.
You can download the tar ball,
R CMD INSTALL on it, or (recommended) use the devtools package to install the development version:
# install devtools if requiredif (!require("devtools")) install.packages("devtools")# then install natdevtools::install_github("jefferis/nat")# then nat.nblastdevtools::install_github("nat.nblast", "jefferislab")
Note: Windows users need Rtools to install this way.