NeuroAnatomy Toolbox ('nat') Extension for Assessing Neuron Similarity and Clustering

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Documentation for package ‘nat.nblast’ version 1.6.7

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

nat.nblast-package	Neuron similarity, search and clustering tools
calc_dists_dotprods	Calculate distances and dot products between two sets of neurons
calc_prob_mat	Calculate probability matrix from distances and dot products between neuron segments
calc_score_matrix	Calculate scoring matrix from probability matrices for matching and non-matching sets of neurons
create_scoringmatrix	Create a scoring matrix given matching and non-matching sets of neurons
diagonal	Extract diagonal terms from a variety of matrix types
diagonal.default	Extract diagonal terms from a variety of matrix types
fctraces20	20 traced Drosophila neurons from Chiang et al 2011
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
nat.nblast	Neuron similarity, search and clustering tools
nblast	Calculate similarity score for neuron morphologies
nblast_allbyall	Wrapper function to compute all by all NBLAST scores for a set of neurons
nblast_allbyall.character	Wrapper function to compute all by all NBLAST scores for a set of neurons
nblast_allbyall.neuronlist	Wrapper function to compute all by all NBLAST scores for a set of neurons
NeuriteBlast	Produce similarity score for neuron morphologies
neuron_pairs	Utility function to generate all or random pairs of neurons
nhclust	Cluster a set of neurons
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
smat.fcwb	Scoring matrices for neuron similarities in FCWB template brain
smat_alpha.fcwb	Scoring matrices for neuron similarities in FCWB template brain
sparse_score_mat	Convert a subset of a square score matrix to a sparse representation
subset.hclust	Return the labels of items in 1 or more groups cut from hclust object
sub_dist_mat	Convert (a subset of) a raw score matrix to a distance matrix
sub_score_mat	Return scores (or distances) for given query and target neurons
WeightedNNBasedLinesetMatching	Compute point & tangent vector similarity score between two linesets
WeightedNNBasedLinesetMatching.dotprops	Compute point & tangent vector similarity score between two linesets
WeightedNNBasedLinesetMatching.neuron	Compute point & tangent vector similarity score between two linesets
[	Extract parts of a sparse 'spam' matrix
[-method	Extract parts of a sparse 'spam' matrix