Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 6 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 5 committers (20.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.6%) to scientific vocabulary
Keywords
Repository
Visualise Clusterings at Different Resolutions
Basic Info
- Host: GitHub
- Owner: lazappi
- License: gpl-3.0
- Language: R
- Default Branch: main
- Homepage: https://lazappi.github.io/clustree/
- Size: 36.9 MB
Statistics
- Stars: 239
- Watchers: 5
- Forks: 15
- Open Issues: 12
- Releases: 8
Topics
Metadata Files
README.md
clustree 
Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualisation for interrogating clusterings as resolution increases.
Installation
You can install the release version of clustree from CRAN with:
r
install.packages("clustree")
If you want to use the development version that can be installed from GitHub
using the remotes package:
``` r
install.packages("remotes")
remotes::install_github("lazappi/clustree@develop") ```
To also build the vignettes use:
``` r
install.packages("remotes")
remotes::installgithub("lazappi/clustree@develop", dependencies = TRUE, buildvignettes = TRUE) ```
NOTE: Building the vignettes requires the installation of additional packages.
Documentation
The documentation for clustree is available from CRAN at https://cran.r-project.org/package=clustree.
To view the vignette and all the package documentation for the development version visit http://lazappi.github.io/clustree.
Citing clustree
If you use clustree or the clustering trees approach in your work please cite our publication "Zappia L, Oshlack A. Clustering trees: a visualization for evaluating clusterings at multiple resolutions. Gigascience. 2018;7. DOI:gigascience/giy083.
``` citation("clustree")
Zappia L, Oshlack A. Clustering trees: a visualization for evaluating clusterings at multiple resolutions. GigaScience. 2018;7. DOI:gigascience/giy083
A BibTeX entry for LaTeX users is
@Article{, author = {Luke Zappia and Alicia Oshlack}, title = {Clustering trees: a visualization for evaluating clusterings at multiple resolutions}, journal = {GigaScience}, volume = {7}, number = {7}, month = {jul}, year = {2018}, url = {http://dx.doi.org/10.1093/gigascience/giy083}, doi = {10.1093/gigascience/giy083}, } ```
Contributors
Thank you to everyone who has contributed code to the clustree package:
- @andreamrau - added the
edge_arrow_endsoption - @mojaveazure - added support for Seurat v3 objects
Owner
- Name: Luke Zappia
- Login: lazappi
- Kind: user
- Website: http://lazappi.id.au
- Twitter: _lazappi_
- Repositories: 61
- Profile: https://github.com/lazappi
Bioinformatics postdoc and R developer (he/him)
GitHub Events
Total
- Issues event: 3
- Watch event: 20
- Issue comment event: 7
- Push event: 1
Last Year
- Issues event: 3
- Watch event: 20
- Issue comment event: 7
- Push event: 1
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Luke Zappia | l****i | 227 |
| Paul Hoffman | m****e | 1 |
| Michel Lang | m****g@g****m | 1 |
| Andrea M Rau | a****u@i****r | 1 |
| Kristoffer Vitting-Seerup | k****i@d****k | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 91
- Total pull requests: 14
- Average time to close issues: about 2 months
- Average time to close pull requests: about 20 hours
- Total issue authors: 58
- Total pull request authors: 5
- Average comments per issue: 2.59
- Average comments per pull request: 1.36
- Merged pull requests: 14
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 2.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- lazappi (30)
- jkanche (2)
- liz-is (2)
- denvercal1234GitHub (2)
- tiagobrc (2)
- Elena983 (1)
- Gesmira (1)
- anos-s (1)
- denertekin (1)
- Polly314 (1)
- rmenafra (1)
- naddsch (1)
- bari89 (1)
- repeatpipettor (1)
- nbartonicek (1)
Pull Request Authors
- lazappi (10)
- mojaveazure (1)
- kvittingseerup (1)
- andreamrau (1)
- mllg (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- cran 3,704 last-month
- Total docker downloads: 1,390
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Total dependent packages: 4
(may contain duplicates) -
Total dependent repositories: 14
(may contain duplicates) - Total versions: 16
- Total maintainers: 1
cran.r-project.org: clustree
Visualise Clusterings at Different Resolutions
- Homepage: https://github.com/lazappi/clustree
- Documentation: http://cran.r-project.org/web/packages/clustree/clustree.pdf
- License: GPL-3
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Latest release: 0.5.1
published over 2 years ago
Rankings
Maintainers (1)
conda-forge.org: r-clustree
- Homepage: https://github.com/lazappi/clustree
- License: GPL-3.0-only
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Latest release: 0.5.0
published over 3 years ago
Rankings
Dependencies
- R >= 3.5 depends
- ggraph * depends
- checkmate * imports
- dplyr * imports
- ggplot2 * imports
- ggrepel * imports
- grid * imports
- igraph * imports
- methods * imports
- rlang * imports
- tidygraph * imports
- viridis * imports
- Seurat >= 2.3.0 suggests
- SingleCellExperiment * suggests
- SummarizedExperiment * suggests
- covr * suggests
- knitr * suggests
- pkgdown * suggests
- rmarkdown * suggests
- spelling * suggests
- testthat >= 2.1.0 suggests