CytoSimplex
Simplex plot showing similarity between single-cells and clusters
Science Score: 39.0%
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
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
○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 (13.7%) to scientific vocabulary
Repository
Simplex plot showing similarity between single-cells and clusters
Basic Info
- Host: GitHub
- Owner: welch-lab
- Language: R
- Default Branch: main
- Size: 18.3 MB
Statistics
- Stars: 5
- Watchers: 2
- Forks: 2
- Open Issues: 1
- Releases: 2
Metadata Files
README.md
CytoSimplex 
CytoSimplex is an R package that creates simplex plot showing similarity between single-cells and terminals represented by clusters of cells. RNA velocity can be added as another layer of information.
For Python users, we have a Python package CytoSimplex that provides the same functionalities.
Installation
The package is developed and tested under R>=4.2.0. Users can install R following the instruction provided on CRAN. RStudio is a recommended IDE for working with R projects.
To install CytoSimplex in R, run the following command in an R console:
R
install.packages("CytoSimplex")
For the latest developmental version, run the following command in an R console:
R
if (!requireNamespace("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github("welch-lab/CytoSimplex")
Tutorial
We have created a documentation website for posting example tutorials walking through the process from loading the provided example data and creating different types of visualization.
Citation
If you used CytoSimplex in your work, please cite the following work published on Bioinformatics:
Jialin Liu, Yichen Wang, Chen Li, Yichen Gu, Noriaki Ono and Joshua D. Welch, CytoSimplex: Visualizing Single-cell Fates and Transitions on a Simplex, 2025, Bioinformatics, (https://doi.org/10.1093/bioinformatics/btaf119)
Owner
- Name: welch-lab
- Login: welch-lab
- Kind: organization
- Repositories: 9
- Profile: https://github.com/welch-lab
GitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 2
- Watch event: 4
- Issue comment event: 4
- Push event: 7
- Pull request event: 2
- Fork event: 2
Last Year
- Create event: 1
- Release event: 1
- Issues event: 2
- Watch event: 4
- Issue comment event: 4
- Push event: 7
- Pull request event: 2
- Fork event: 2
Packages
- Total packages: 1
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Total downloads:
- cran 586 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 3
- Total maintainers: 1
cran.r-project.org: CytoSimplex
Simplex Visualization of Cell Fate Similarity in Single-Cell Data
- Homepage: https://welch-lab.github.io/CytoSimplex/
- Documentation: http://cran.r-project.org/web/packages/CytoSimplex/CytoSimplex.pdf
- License: GPL-3
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Latest release: 0.2.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v3 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- R >= 3.6 depends
- methods * depends
- stats * depends
- Matrix * imports
- Rcpp * imports
- ggplot2 * imports
- plot3D * imports
- rlang * imports
- Seurat * suggests
- SeuratObject * suggests
- SingleCellExperiment * suggests
- SummarizedExperiment * suggests
- knitr * suggests
- magick * suggests
- patchwork * suggests
- rgl * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests