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.

AuthorGreg Jefferis and James Manton
Date of publication2016-04-26 16:50:45
MaintainerJames Manton <ajd.manton@googlemail.com>
LicenseGPL-3
Version1.6.2

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...

Functions

[ Man page
calc_dists_dotprods Man page
calc_prob_mat Man page
calc_score_matrix Man page
create_scoringmatrix Man page
diagonal Man page
diagonal.default Man page
fctraces20 Man page
fill_in_sparse_score_mat Man page
fill_pairs_sparse_score_mat Man page
nat.nblast Man page
nat.nblast-package Man page
nblast Man page
nblast_allbyall Man page
nblast_allbyall.character Man page
nblast_allbyall.neuronlist Man page
NeuriteBlast Man page
neuron_pairs Man page
nhclust Man page
plot3d.hclust Man page
show_similarity Man page
smat_alpha.fcwb Man page
smat.fcwb Man page
[,spam,character,character,logical-method Man page
[,spam,character,character,missing-method Man page
[,spam,character,missing,logical-method Man page
[,spam,character,missing,missing-method Man page
[,spam,missing,character,logical-method Man page
[,spam,missing,character,missing-method Man page
sparse_score_mat Man page
sub_dist_mat Man page
sub_score_mat Man page
subset.hclust Man page
WeightedNNBasedLinesetMatching Man page
WeightedNNBasedLinesetMatching.dotprops Man page
WeightedNNBasedLinesetMatching.neuron Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.