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

Extends package 'nat' (NeuroAnatomy Toolbox) by providing a collection of NBLAST-related functions.

Author
Greg Jefferis and James Manton
Date of publication
2016-04-26 16:50:45
Maintainer
James Manton <ajd.manton@googlemail.com>
License
GPL-3
Version
1.6.2

View on CRAN

Man pages

calc_dists_dotprods
Calculate distances and dot products between two sets of...
calc_prob_mat
Calculate probability matrix from distances and dot products...
calc_score_matrix
Calculate scoring matrix from probability matrices for...
create_scoringmatrix
Create a scoring matrix given matching and non-matching sets...
diagonal
Extract diagonal terms from a variety of matrix types
extract-methods
Extract parts of a sparse 'spam' matrix
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...
nat.nblast-package
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...
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...
show_similarity
Display two neurons with segments coloured by similarity
smat.fcwb
Scoring matrices for neuron similarities in FCWB template...
sparse_score_mat
Convert a subset of a square score matrix to a sparse...
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...
subset.hclust
Return the labels of items in 1 or more groups cut from...
WeightedNNBasedLinesetMatching
Compute point & tangent vector similarity score between two...

Files in this package

nat.nblast
nat.nblast/inst
nat.nblast/inst/doc
nat.nblast/inst/doc/NBLAST-Clustering.html
nat.nblast/inst/doc/NBLAST-Clustering.Rmd
nat.nblast/inst/doc/NBLAST-Clustering.R
nat.nblast/tests
nat.nblast/tests/testthat
nat.nblast/tests/testthat/test-NBLAST1.r
nat.nblast/tests/testthat/test-NBLAST2.r
nat.nblast/tests/testthat/test-scoremats.r
nat.nblast/tests/testthat/test-clustering.r
nat.nblast/tests/testthat/test-smat.r
nat.nblast/tests/testthat/testdata
nat.nblast/tests/testthat/testdata/testneurons.rds
nat.nblast/tests/test-all.R
nat.nblast/NAMESPACE
nat.nblast/NEWS
nat.nblast/data
nat.nblast/data/smat_alpha.fcwb.rda
nat.nblast/data/smat.fcwb.rda
nat.nblast/data/fctraces20.rda
nat.nblast/R
nat.nblast/R/neuriteblast.r
nat.nblast/R/scoremats.r
nat.nblast/R/spam.r
nat.nblast/R/DATA.r
nat.nblast/R/similarity.r
nat.nblast/R/zzz.r
nat.nblast/R/clustering.r
nat.nblast/R/smat.r
nat.nblast/R/nat.nblast.r
nat.nblast/vignettes
nat.nblast/vignettes/NBLAST-Clustering.Rmd
nat.nblast/README.md
nat.nblast/MD5
nat.nblast/build
nat.nblast/build/vignette.rds
nat.nblast/DESCRIPTION
nat.nblast/man
nat.nblast/man/sparse_score_mat.Rd
nat.nblast/man/nblast_allbyall.Rd
nat.nblast/man/subset.hclust.Rd
nat.nblast/man/fctraces20.Rd
nat.nblast/man/WeightedNNBasedLinesetMatching.Rd
nat.nblast/man/nblast.Rd
nat.nblast/man/sub_dist_mat.Rd
nat.nblast/man/plot3d.hclust.Rd
nat.nblast/man/extract-methods.Rd
nat.nblast/man/show_similarity.Rd
nat.nblast/man/fill_pairs_sparse_score_mat.Rd
nat.nblast/man/NeuriteBlast.Rd
nat.nblast/man/calc_score_matrix.Rd
nat.nblast/man/smat.fcwb.Rd
nat.nblast/man/diagonal.Rd
nat.nblast/man/create_scoringmatrix.Rd
nat.nblast/man/nhclust.Rd
nat.nblast/man/neuron_pairs.Rd
nat.nblast/man/calc_dists_dotprods.Rd
nat.nblast/man/fill_in_sparse_score_mat.Rd
nat.nblast/man/nat.nblast-package.Rd
nat.nblast/man/calc_prob_mat.Rd
nat.nblast/man/sub_score_mat.Rd