dendextend

Extending R's Dendrogram Functionality

https://github.com/talgalili/dendextend

Science Score: 49.0%

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

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README
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Academic publication links
✓
Committers with academic emails
2 of 20 committers (10.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.4%) to scientific vocabulary

Keywords from Contributors

shiny bioinformatics d3-heatmap dendextend dendrogram heatmap plotly

Last synced: 6 months ago · JSON representation

Repository

Extending R's Dendrogram Functionality

Basic Info

Host: GitHub
Owner: talgalili
Language: R
Default Branch: master
Homepage:
Size: 76 MB

Statistics

Stars: 155
Watchers: 12
Forks: 29
Open Issues: 58
Releases: 4

Created almost 13 years ago · Last pushed 8 months ago

Metadata Files

Readme Changelog

dendextend

dendextend website (built using pkgdown)

Table of contents:

Introduction
Installation
Usage
Getting help
How to cite the dendextend package
Submitting bug reports and patches

Introduction

Class "dendrogram" provides general functions for handling tree-like structures in R. It is intended as a replacement for similar functions in hierarchical clustering and classification/regression trees, such that all of these can use the same engine for plotting or cutting trees.

However, many basic features are still missing from the dendrogram class. This package aims at filling in some gaps.

The dendextend package extending R core dendrogram functions.

Installation

To install and load dendextend, simply use:

r install.packages('dendextend') # stable CRAN version library("dendextend") # load the package

Usage

Vignettes:

Also ceck out the dendextend tag in stackoverflow for more examples.

A notable sister package for dendextend is heatmaply for creating interactive cluster heatmaps using R (combining dendextend and plotly).

Getting help

Please post your question to stackoverflow using the tags: dendextend and r.

How to cite the dendextend package

The methods within the code package can be cited as:

 Tal Galili (2015). dendextend: an R package for visualizing, adjusting, and comparing trees of
 hierarchical clustering. Bioinformatics. DOI: 10.1093/bioinformatics/btv428

A BibTeX entry for LaTeX users is

 @Article{,
   author = {Tal Galili},
   title = {dendextend: an R package for visualizing, adjusting, and comparing trees of hierarchical clustering},
   journal = {Bioinformatics},
   year = {2015},
   doi = {10.1093/bioinformatics/btv428},
   url = {https://doi.org/10.1093/bioinformatics/btv428},
   eprint = {https://academic.oup.com/bioinformatics/article-pdf/31/22/3718/17122682/btv428.pdf},
 }

This free open-source software implements academic research by the authors and co-workers. If you use it, please support the project by citing the appropriate journal articles.

Submitting bug reports and patches

You are welcome to:

submit bug-reports and features' suggestions at: https://github.com/talgalili/dendextend/issues
send a pull request on: https://github.com/talgalili/dendextend/
compose a friendly e-mail to: tal.galili@gmail.com

Before reporting bugs, please make sure you're using the latest version from github:

```R install.packages.2 <- function (pkg) { if (!require(pkg, character.only = TRUE)) install.packages(pkg, character.only = TRUE) } install.packages('remotes') remotes::install_github('talgalili/dendextend')

Having colorspace is also useful, since it is used

In various examples in the vignettes

install.packages.2('colorspace') ```

Latest news

You can see the most recent changes to the package in the NEWS.md file

Code of conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Owner

Name: Tal Galili
Login: talgalili
Kind: user
Location: Tel aviv, Israel
Company: Tel Aviv University

Website: https://www.r-statistics.com
Repositories: 20
Profile: https://github.com/talgalili

GitHub Events

Total

Create event: 2
Commit comment event: 4
Release event: 2
Issues event: 13
Watch event: 5
Issue comment event: 82
Push event: 57
Pull request review event: 8
Pull request review comment event: 8
Pull request event: 46
Fork event: 1

Last Year

Create event: 2
Commit comment event: 4
Release event: 2
Issues event: 13
Watch event: 5
Issue comment event: 82
Push event: 57
Pull request review event: 8
Pull request review comment event: 8
Pull request event: 46
Fork event: 1

Committers

Last synced: 9 months ago

All Time

Total Commits: 1,202
Total Committers: 20
Avg Commits per committer: 60.1
Development Distribution Score (DDS): 0.075

Past Year

Commits: 49
Committers: 3
Avg Commits per committer: 16.333
Development Distribution Score (DDS): 0.51

Top Committers

Name	Email	Commits
Tal Galili	t**i@g**m	1,112
Alec Buetow	9****w	24
Cath	C****G	14
samperochkin	s**3@u**a	11
C2H4	b**3@g**m	10
Chase Clark	c**2@u**u	5
Hummel	h**a@a**e	4
mark	m**o@g**m	4
Alan O'Callaghan	a**n@o**m	3
Chase Clark	1****c	2
David Bradley	8****7	2
houyun	h**g@1**m	2
Lucas Gray	s**t@g**m	2
John Ma	J****a	1
Julien	j**n@n**g	1
Michael Chirico	m**4@g**m	1
storaged	k**k@s**l	1
Alan O'Callaghan	a**n@f**m	1
jdetribol	4****l	1
pschupp	3****p	1

Committer Domains (Top 20 + Academic)

fiosgenomics.com: 1 storaged.mimuw.edu.pl: 1 nozav.org: 1 163.com: 1 ad.dkfz-heidelberg.de: 1 uic.edu: 1 ulaval.ca: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 91
Total pull requests: 41
Average time to close issues: 7 months
Average time to close pull requests: 27 days
Total issue authors: 59
Total pull request authors: 16
Average comments per issue: 2.34
Average comments per pull request: 3.15
Merged pull requests: 38
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 6
Pull requests: 22
Average time to close issues: about 1 month
Average time to close pull requests: about 11 hours
Issue authors: 5
Pull request authors: 2
Average comments per issue: 4.33
Average comments per pull request: 2.36
Merged pull requests: 21
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

talgalili (33)
mooibroekd (2)
ghost (2)
MaximilianStammnitz (2)
TreeT2 (2)
rec3141 (1)
Jigyasa3 (1)
slizarazo21 (1)
Mshoukat1992 (1)
ndrubins (1)
sventura (1)
wenjingcui (1)
aravind-j (1)
zvittorio (1)
theclue (1)

Pull Request Authors

alecbuetow (44)
Alanocallaghan (4)
chasemc (3)
MichaelChirico (2)
pschupp (1)
SplitInf (1)
samperochkin (1)
jdetribol (1)
storaged (1)
JohnMCMa (1)
hummelma (1)
hypercompetent (1)
DBradley27 (1)
ghost (1)
CathG (1)

Top Labels

Issue Labels

bug (15) enhancement (9)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 67,886 last-month
Total docker downloads: 249,718

Total dependent packages: 71
Total dependent repositories: 188
Total versions: 33
Total maintainers: 1

cran.r-project.org: dendextend

Extending 'dendrogram' Functionality in R

Homepage: https://talgalili.github.io/dendextend/
Documentation: http://cran.r-project.org/web/packages/dendextend/dendextend.pdf
License: GPL-2 | GPL-3
Latest release: 1.19.1
published 8 months ago

Versions: 33
Dependent Packages: 71
Dependent Repositories: 188
Downloads: 67,886 Last month
Docker Downloads: 249,718

Rankings

Dependent packages count: 1.3%

Dependent repos count: 1.3%

Downloads: 1.6%

Forks count: 2.7%

Stargazers count: 2.8%

Average: 4.5%

Docker downloads count: 17.3%

Maintainers (1)

tal.galili@gmail.com

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 3.0.0 depends
Hmisc * enhances
WGCNA * enhances
data.table * enhances
dendroextras * enhances
distory * enhances
ggdendro * enhances
moduleColor * enhances
phangorn * enhances
rpart * enhances
zoo * enhances
datasets * imports
ggplot2 * imports
magrittr >= 1.0.1 imports
stats * imports
utils * imports
viridis * imports
DendSer * suggests
MASS * suggests
ape * suggests
circlize >= 0.2.5 suggests
cluster * suggests
colorspace * suggests
corrplot * suggests
covr * suggests
dynamicTreeCut * suggests
fpc * suggests
gplots * suggests
heatmaply * suggests
knitr * suggests
microbenchmark * suggests
pvclust * suggests
rmarkdown * suggests
seriation * suggests
testthat * suggests

dendextend

Science Score: 49.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.md

dendextend

Introduction

Installation

Usage

Getting help

How to cite the dendextend package

Submitting bug reports and patches

Having colorspace is also useful, since it is used

In various examples in the vignettes

Latest news

Code of conduct

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: dendextend

Rankings

Maintainers (1)

Dependencies