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

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

## Documentation for package ‘nat.nblast’ version 1.6.9

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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