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nat.nblast (version 1.5)
NeuroAnatomy Toolbox (nat) Extension for Assessing Neuron Similarity and Clustering
Description
Extends package nat (NeuroAnatomy Toolbox) by providing a collection of NBLAST-related functions.
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Version
1.6.7
1.6.5
1.6.2
1.5
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Install
install.packages('nat.nblast')
Monthly Downloads
207
Version
1.5
License
GPL-3
Maintainer
James Manton
Last Published
September 19th, 2014
Functions in nat.nblast (1.5)
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Extract parts of a sparse
spam
matrix
fctraces20
20 traced Drosophila neurons from Chiang et al 2011
WeightedNNBasedLinesetMatching
Compute point & tangent vector similarity score between two linesets
calc_dists_dotprods
Calculate distances and dot products between two sets of neurons
neuron_pairs
Utility function to generate all or random pairs of neurons
nblast
Calculate similarity score for neuron morphologies
fill_in_sparse_score_mat
Add one or more submatrices to a sparse score matrix
nblast_allbyall
Wrapper function to compute all by all NBLAST scores for a set of neurons
fill_pairs_sparse_score_mat
Add forwards, reverse and self scores for a pair of neurons to a sparse score matrix
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
smat.fcwb
Scoring matrices for neuron similarities in FCWB template brain
NeuriteBlast
Produce similarity score for neuron morphologies
subset.hclust
Return the labels of items in 1 or more groups cut from hclust object
calc_prob_mat
Calculate probability matrix from distances and dot products between neuron segments
diagonal
Extract diagonal terms from a variety of matrix types
show_similarity
Display two neurons with segments coloured by similarity
nhclust
Cluster a set of neurons
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
nat.nblast-package
Neuron similarity, search and clustering tools
sparse_score_mat
Convert a subset of a square score matrix to a sparse representation
plot3d.hclust
Methods to identify and plot groups of neurons cut from an hclust object