Package: nat.nblast 1.6.7

Gregory Jefferis

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 for neuronal morphology comparison (Costa et al. (2016) <doi:10.1016/j.neuron.2016.06.012>).

Authors:Gregory Jefferis [aut, cre], James Manton [aut]

nat.nblast_1.6.7.tar.gz
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nat.nblast.pdf |nat.nblast.html✨
nat.nblast/json (API)
NEWS

# Install 'nat.nblast' in R:
install.packages('nat.nblast', repos = c('https://natverse.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/natverse/nat.nblast/issues

Datasets:
  • fctraces20 - 20 traced Drosophila neurons from Chiang et al 2011
  • smat.fcwb - Scoring matrices for neuron similarities in FCWB template brain
  • smat_alpha.fcwb - Scoring matrices for neuron similarities in FCWB template brain

On CRAN:

morphological-analysisnblastneuroanatomyneuroanatomy-toolboxneurons

17 exports 16 stars 2.27 score 56 dependencies 2 mentions 85 scripts 221 downloads

Last updated 17 days agofrom:3dd3b5b8f6. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 31 2024
R-4.5-winNOTEAug 31 2024
R-4.5-linuxNOTEAug 31 2024
R-4.4-winOKAug 31 2024
R-4.4-macOKAug 31 2024
R-4.3-winOKAug 31 2024
R-4.3-macOKAug 31 2024

Exports:calc_dists_dotprodscalc_prob_matcalc_score_matrixcreate_scoringmatrixdiagonalfill_in_sparse_score_matfill_pairs_sparse_score_matnblastnblast_allbyallNeuriteBlastneuron_pairsnhclustshow_similaritysparse_score_matsub_dist_matsub_score_matWeightedNNBasedLinesetMatching

Dependencies:backportsbase64encBHbslibcachemcheckmateclicpp11crayondendroextrasdigestdotCall64evaluatefastmapfilehashfontawesomefsgluehighrhmshtmltoolshtmlwidgetsigraphjquerylibjsonliteknitrlatticelifecyclemagrittrMatrixmemoisemimenabornatnat.utilspbapplypkgconfigplyrprettyunitsprogressR6rappdirsRcppRcppEigenrglrlangrmarkdownsassspamstringistringrtinytexvctrsxfunyamlzip

NBLAST Clustering

Gregory Jefferis

Rendered fromNBLAST-Clustering.Rmdusingknitr::rmarkdownon Aug 31 2024.

Last update: 2016-07-01
Started: 2015-11-06

Readme and manuals

Help Manual

Help pageTopics
Neuron similarity, search and clustering toolsnat.nblast-package nat.nblast
Extract parts of a sparse 'spam' matrix[ [,spam,character,character,logical-method [,spam,character,character,missing-method [,spam,character,missing,logical-method [,spam,character,missing,missing-method [,spam,missing,character,logical-method [,spam,missing,character,missing-method
Calculate distances and dot products between two sets of neuronscalc_dists_dotprods
Calculate probability matrix from distances and dot products between neuron segmentscalc_prob_mat
Calculate scoring matrix from probability matrices for matching and non-matching sets of neuronscalc_score_matrix
Create a scoring matrix given matching and non-matching sets of neuronscreate_scoringmatrix
Extract diagonal terms from a variety of matrix typesdiagonal diagonal.default
20 traced Drosophila neurons from Chiang et al 2011fctraces20
Add one or more submatrices to a sparse score matrixfill_in_sparse_score_mat
Add forwards, reverse and self scores for a pair of neurons to a sparse score matrixfill_pairs_sparse_score_mat
Calculate similarity score for neuron morphologiesnblast
Wrapper function to compute all by all NBLAST scores for a set of neuronsnblast_allbyall nblast_allbyall.character nblast_allbyall.neuronlist
Produce similarity score for neuron morphologiesNeuriteBlast
Utility function to generate all or random pairs of neuronsneuron_pairs
Cluster a set of neuronsnhclust
Methods to identify and plot groups of neurons cut from an 'hclust' objectplot3d.hclust
Display two neurons with segments in the query coloured by similarityshow_similarity
Scoring matrices for neuron similarities in FCWB template brainsmat.fcwb smat_alpha.fcwb
Convert a subset of a square score matrix to a sparse representationsparse_score_mat
Convert (a subset of) a raw score matrix to a distance matrixsub_dist_mat
Return scores (or distances) for given query and target neuronssub_score_mat
Return the labels of items in 1 or more groups cut from hclust objectsubset.hclust
Compute point & tangent vector similarity score between two linesetsWeightedNNBasedLinesetMatching WeightedNNBasedLinesetMatching.dotprops WeightedNNBasedLinesetMatching.neuron