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nat

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

https://github.com/natverse/nat

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 18 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: nature.com
  • ✓
    Committers with academic emails
    3 of 12 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.6%) to scientific vocabulary

Keywords

3d connectomics cran image-analysis neuroanatomy neuroanatomy-toolbox neuron neuron-morphology neuroscience r visualisation
Last synced: 6 months ago · JSON representation

Repository

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

Basic Info
Statistics
  • Stars: 69
  • Watchers: 17
  • Forks: 27
  • Open Issues: 60
  • Releases: 26
Topics
3d connectomics cran image-analysis neuroanatomy neuroanatomy-toolbox neuron neuron-morphology neuroscience r visualisation
Created about 12 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Code of conduct

README.md

nat: NeuroAnatomy Toolbox

natverse DOI Release Version CRAN_Status_Badge R-CMD-check Coverage Status Docs Downloads <!-- badges: end -->

An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons. nat is the core package of a wider suite of neuroanatomy tools introduced at http://natverse.github.io. nat (and its ancestors) have been used in a number of papers from our group including:

Cell 2007 Cover CB 2010 Cover Food and Pheromone Integration Cell 2013 Abstract Neuron 2016

Quick Start

For the impatient ...

```r

install

install.packages("nat")

use

library(nat)

plot some test data (?kcs20 for details)

Drosophila Kenyon cells processed from raw data formerly available at

flycircuit.tw

head(kcs20) open3d() plot3d(kcs20, col=type)

get help

?nat ```

Installation

A confirmed stable version of nat can be installed from CRAN.

r install.packages("nat") `

However, nat remains under quite active development, so if you will be using nat extensively, we generally recommend installing the latest development version directly from github using the devtools package.

```r

install devtools if required

if (!requireNamespace("devtools")) install.packages("devtools")

then install nat

devtools::install_github("natverse/nat")

```

Learn

To get an idea of what nat can do:

When you're ready to learn more:

Help

If you want some help using nat:

  • For installation issues, see the Installation vignette
  • Contact nat-user Google group - we normally respond promptly and you will also be helping future users.

If you think that you have found a bug:

  • Install the development version of nat using devtools (see above) and see if that helps.
  • Check the github issues and
    • file a bug report if this seems to be a new problem
    • comment on an existing bug report

Thanks for your interest in nat!

Owner

  • Name: natverse
  • Login: natverse
  • Kind: organization

R tools for quantitative neuroanatomy

GitHub Events

Total
  • Watch event: 3
  • Push event: 7
  • Pull request event: 1
  • Create event: 3
Last Year
  • Watch event: 3
  • Push event: 7
  • Pull request event: 1
  • Create event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 2,526
  • Total Committers: 12
  • Avg Commits per committer: 210.5
  • Development Distribution Score (DDS): 0.123
Past Year
  • Commits: 11
  • Committers: 2
  • Avg Commits per committer: 5.5
  • Development Distribution Score (DDS): 0.091
Top Committers
Name Email Commits
Gregory Jefferis j****s@g****m 2,216
James Manton a****n@g****m 116
Sri j****n@g****m 98
Dominik Krzeminski d****3@c****k 57
alexanderbates a****s@g****m 27
dokato r****2@g****m 4
Marta Costa m****6@c****k 3
istvantaisz i****z@g****m 1
zhihaozheng z****n@g****m 1
Jonathan Marty j****y@g****m 1
Ben Sutcliffe s****f@m****k 1
Duncan Murdoch m****n@g****m 1
Committer Domains (Top 20 + Academic)
cam.ac.uk: 2 mrc-lmb.cam.ac.uk: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 46
  • Total pull requests: 60
  • Average time to close issues: 3 months
  • Average time to close pull requests: 30 days
  • Total issue authors: 12
  • Total pull request authors: 7
  • Average comments per issue: 1.83
  • Average comments per pull request: 2.7
  • Merged pull requests: 46
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 4
  • Average time to close issues: about 2 hours
  • Average time to close pull requests: 4 days
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 11.0
  • Average comments per pull request: 1.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jefferis (20)
  • dokato (11)
  • SridharJagannathan (4)
  • Jsalas424 (3)
  • kjheinz (1)
  • szhorvat (1)
  • PostPreAndCleft (1)
  • artxz (1)
  • dempseyg447 (1)
  • mmc46 (1)
  • alexanderbates (1)
Pull Request Authors
  • jefferis (32)
  • dokato (21)
  • SridharJagannathan (4)
  • alexanderbates (3)
  • jonmarty (1)
  • schlegelp (1)
  • dmurdoch (1)
Top Labels
Issue Labels
enhancement (5) bug (2) question (1) wontfix (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 443 last-month
  • Total docker downloads: 74
  • Total dependent packages: 5
    (may contain duplicates)
  • Total dependent repositories: 27
    (may contain duplicates)
  • Total versions: 78
  • Total maintainers: 1
proxy.golang.org: github.com/natverse/nat
  • Versions: 53
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 9.0%
Average: 9.6%
Dependent repos count: 10.2%
Last synced: 7 months ago
cran.r-project.org: nat

NeuroAnatomy Toolbox for Analysis of 3D Image Data

  • Versions: 25
  • Dependent Packages: 5
  • Dependent Repositories: 27
  • Downloads: 443 Last month
  • Docker Downloads: 74
Rankings
Forks count: 3.2%
Dependent repos count: 5.3%
Stargazers count: 5.9%
Dependent packages count: 8.2%
Average: 10.6%
Downloads: 17.8%
Docker downloads count: 23.3%
Maintainers (1)
jefferis@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.15.1 depends
  • rgl >= 0.98.1 depends
  • natcpp * enhances
  • checkmate * imports
  • digest * imports
  • filehash >= 2.3 imports
  • igraph >= 0.7.1 imports
  • methods * imports
  • nabor * imports
  • nat.utils >= 0.4.2 imports
  • pbapply * imports
  • plyr * imports
  • progress * imports
  • stringr * imports
  • yaml * imports
  • zip * imports
  • MASS * suggests
  • Morpho * suggests
  • Rvcg >= 0.17 suggests
  • XML * suggests
  • alphashape3d * suggests
  • brotli * suggests
  • httr * suggests
  • jsonlite * suggests
  • knitr * suggests
  • plotly * suggests
  • qs * suggests
  • readobj * suggests
  • rmarkdown * suggests
  • spelling * suggests
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/upload-artifact v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite