Reference

Package Overview Provides an overview of key functions and classes
nat.nblast-package	Neuron similarity, search and clustering tools
Key functions The main entry points to neuron search and clustering
nblast()	Calculate similarity score for neuron morphologies
nblast_allbyall()	Wrapper function to compute all by all NBLAST scores for a set of neurons
nhclust()	Cluster a set of neurons
Plotting results Visualise pairwise neuron search or clustering results
plot3d(<hclust>)	Methods to identify and plot groups of neurons cut from an hclust object
show_similarity()	Display two neurons with segments in the query coloured by similarity
subset(<hclust>)	Return the labels of items in 1 or more groups cut from hclust object
Scoring Matrices Calculate the scoring matrices that define NBLAST similarity
create_scoringmatrix()	Create a scoring matrix given matching and non-matching sets of neurons
calc_score_matrix()	Calculate scoring matrix from probability matrices for matching and non-matching sets of neurons
calc_prob_mat()	Calculate probability matrix from distances and dot products between neuron segments
calc_dists_dotprods()	Calculate distances and dot products between two sets of neurons
smat.fcwb	Scoring matrices for neuron similarities in FCWB template brain
Mid level functions for result matrices Functions that you might use to manipulate matrices containing all by all NBLAST results for use with other clustering strategies (besides nhclust)
sub_score_mat()	Return scores (or distances) for given query and target neurons
sub_dist_mat()	Convert (a subset of) a raw score matrix to a distance matrix
sparse_score_mat()	Convert a subset of a square score matrix to a sparse representation
Low level search functions Intended for developer use
NeuriteBlast()	Produce similarity score for neuron morphologies
neuron_pairs()	Utility function to generate all or random pairs of neurons
WeightedNNBasedLinesetMatching()	Compute point & tangent vector similarity score between two linesets
fctraces20	20 traced Drosophila neurons from Chiang et al 2011
Matrix utility functions Intended for developer use
diagonal()	Extract diagonal terms from a variety of matrix types
`[`(<spam>,<character>,<character>,<logical>) `[`(<spam>,<character>,<character>,<missing>) `[`(<spam>,<character>,<missing>,<logical>) `[`(<spam>,<character>,<missing>,<missing>) `[`(<spam>,<missing>,<character>,<logical>) `[`(<spam>,<missing>,<character>,<missing>)	Extract parts of a sparse spam matrix
fill_in_sparse_score_mat()	Add one or more submatrices to a sparse score matrix
fill_pairs_sparse_score_mat()	Add forwards, reverse and self scores for a pair of neurons to a sparse score matrix