package-cancerevolutionvisualization
Publication Quality Phylogenetic Tree Plots
https://github.com/uclahs-cds/package-cancerevolutionvisualization
Science Score: 26.0%
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
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.7%) to scientific vocabulary
Repository
Publication Quality Phylogenetic Tree Plots
Basic Info
- Host: GitHub
- Owner: uclahs-cds
- License: gpl-2.0
- Language: R
- Default Branch: main
- Homepage: https://cran.r-project.org/web/packages/CancerEvolutionVisualization/
- Size: 1.39 MB
Statistics
- Stars: 2
- Watchers: 7
- Forks: 0
- Open Issues: 22
- Releases: 1
Metadata Files
README.md
CancerEvolutionVisualization
Description
CancerEvolutionVisualization (CEV) generates tree plots with precise branch lengths, gene annotations, and cellular prevalence. The package handles complex tree structures (angles, lengths, etc.) and can be further refined as needed by the user. These functions will give users great ease of use and customization options in broad use for biomedical applications, as well as general purpose plotting. Each of the functions also provides valid default settings to make plotting data more efficient and producing high quality plots with standard colour schemes simpler. All functions within this package are capable of producing plots that are of the quality to be presented in scientific publications and journals.
Installation
To install the latest public release of CancerEvolutionVisualization from CRAN:
install.packages("CancerEvolutionVisualization")
Or to install the latest development version from GitHub: ```
install.packages("devtools")
devtools::install_github("uclahs-cds/package-CancerEvolutionVisualization") ```
Resources
Available resources on CEV usage can be found at the package CRAN page, reference manual, and user guide.
Getting help
Looking for guidance or support with CEV? Check out our Discussions page.
Submit bugs, suggest new features or see current works at our Issues page.
Pull requests are also open for discussion.
Contributors
For a full list of contributors please visit the package's page on CRAN
License
Authors: Adriana Salcedo, Dan Knight, Helena Winata & Paul C. Boutros (PBoutros@mednet.ucla.edu)
CancerEvolutionVisualization is licensed under the GNU General Public License version 2. See the file LICENSE.md for the terms of the GNU GPL license.
CancerEvolutionVisualization is a software package for generating publication-quality, customizable plots.
Copyright (C) 2021-2023 University of California Los Angeles ("Boutros Lab") All rights reserved.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Owner
- Name: UCLA JCCC - Cancer Data Science
- Login: uclahs-cds
- Kind: organization
- Email: pboutros@mednet.ucla.edu
- Location: United States of America
- Website: https://cancer.ucla.edu/
- Twitter: theboutroslab
- Repositories: 14
- Profile: https://github.com/uclahs-cds
GitHub Events
Total
- Issues event: 30
- Delete event: 22
- Member event: 1
- Issue comment event: 34
- Push event: 129
- Pull request review comment event: 23
- Pull request event: 43
- Pull request review event: 45
- Create event: 21
Last Year
- Issues event: 30
- Delete event: 22
- Member event: 1
- Issue comment event: 34
- Push event: 129
- Pull request review comment event: 23
- Pull request event: 43
- Pull request review event: 45
- Create event: 21
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 4
- Total pull requests: 16
- Average time to close issues: 2 months
- Average time to close pull requests: about 1 month
- Total issue authors: 1
- Total pull request authors: 4
- Average comments per issue: 0.5
- Average comments per pull request: 0.25
- Merged pull requests: 11
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 15
- Average time to close issues: 2 months
- Average time to close pull requests: 29 days
- Issue authors: 1
- Pull request authors: 4
- Average comments per issue: 0.5
- Average comments per pull request: 0.27
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dan-knight (18)
- whelena (14)
- maotian06 (2)
- nwiltsie (1)
Pull Request Authors
- whelena (22)
- dan-knight (19)
- WuSelina (2)
- aholmes (2)
- nwiltsie (1)
- graceooh (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 222 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
cran.r-project.org: CancerEvolutionVisualization
Publication Quality Phylogenetic Tree Plots
- Homepage: https://github.com/uclahs-cds/package-CancerEvolutionVisualization
- Documentation: http://cran.r-project.org/web/packages/CancerEvolutionVisualization/CancerEvolutionVisualization.pdf
- License: GPL-2
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Latest release: 2.0.1
published over 2 years ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v2 composite
- docker://ghcr.io/uclahs-cds/cicd-base latest composite
- r-lib/actions/setup-tinytex v2 composite
- uclahs-cds/tool-R-CMD-check-action CEV composite
- R >= 3.5.0 depends
- graphics * depends
- grid * depends
- gridExtra * depends
- gtable * depends
- BoutrosLab.plotting.general * imports
- grDevices * imports
- plyr * imports
- stringr * imports
- utils * imports
- knitr * suggests
- testthat * suggests