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 |