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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

Install

install.packages('nat.nblast')

Monthly Downloads

174

Version

1.5

License

GPL-3

Maintainer

James Manton

Last Published

September 19th, 2014

Functions in nat.nblast (1.5)

[

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