Science Score: 36.0%
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
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✓DOI references
Found 1 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 14 committers (7.1%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.1%) to scientific vocabulary
Keywords from Contributors
Repository
Basic Info
- Host: GitHub
- Owner: TrigosTeam
- License: artistic-2.0
- Language: R
- Default Branch: main
- Homepage: https://trigosteam.github.io/SPIAT/
- Size: 34.5 MB
Statistics
- Stars: 24
- Watchers: 4
- Forks: 8
- Open Issues: 4
- Releases: 1
Metadata Files
README.md
SPIAT - Spatial Image Analysis of Tissues
SPIAT (Spatial Image Analysis of Tissues) is an R package with a suite of data processing, quality control, visualization, data handling and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes.
SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.
Installation
To install this package, start R and enter:
r
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SPIAT")
You can also install the latest development version from Github.
r
if (!requireNamespace("devtools", quietly = TRUE)) {
install.packages("devtools")}
devtools::install_github("TrigosTeam/SPIAT")
The estimated installation time on a Windows 10 (64-bit) system is 1.5 minutes.
Vignette
The vignette with an overview of the package can be accessed from the top Menu under Articles or by clicking here.
Issues
Please open an issue on our Github page (https://github.com/TrigosTeam/SPIAT/issues) if you have any questions.
Authors of the package
Yuzhou Feng, Tianpei Yang, Volkan Ozcoban, Mabel Li and John Zhu developed the package, including developing algorithms, writing code and designing the package. Yuzhou Feng and Maria Doyle did the package cleaning and wrote the tutorial. Anna Trigos conceived, supervised the work, developed algorithms and designed the package.
Paper reference
Please check our latest paper for more information!
Yuzhou Feng et al, Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments, Nature Communications (2023). DOI: 10.1038/s41467-023-37822-0
Owner
- Name: Anna Trigos Team at the Peter MacCallum Cancer Centre
- Login: TrigosTeam
- Kind: organization
- Location: Australia
- Repositories: 3
- Profile: https://github.com/TrigosTeam
Prostate cancer/Spatial analysis/Bioinformatics
GitHub Events
Total
- Issues event: 4
- Watch event: 3
- Issue comment event: 2
- Push event: 7
- Pull request event: 4
- Fork event: 1
- Create event: 1
Last Year
- Issues event: 4
- Watch event: 3
- Issue comment event: 2
- Push event: 7
- Pull request event: 4
- Fork event: 1
- Create event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Maria Doyle | m****e@p****g | 534 |
| fuerzhou | 6****3@q****m | 399 |
| fuerzhou | “****3@q****” | 398 |
| cancer-evolution | a****s@p****g | 46 |
| fuerzhou | y****0@g****m | 46 |
| johnzhu997 | 7****7 | 26 |
| Anna Trigos | 1****s | 7 |
| Peter Hickey | p****y@g****m | 3 |
| Anna Trigos | a****s@p****u | 2 |
| CainLachlan | l****n@p****u | 2 |
| Anna Trigos | a****s@v****u | 2 |
| J Wokaty | j****y | 2 |
| J Wokaty | j****y@s****u | 2 |
| rubak | r****k@m****k | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 26
- Total pull requests: 20
- Average time to close issues: 2 months
- Average time to close pull requests: 1 day
- Total issue authors: 18
- Total pull request authors: 6
- Average comments per issue: 2.0
- Average comments per pull request: 0.2
- Merged pull requests: 18
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 5
- Average time to close issues: about 1 month
- Average time to close pull requests: less than a minute
- Issue authors: 6
- Pull request authors: 1
- Average comments per issue: 1.5
- Average comments per pull request: 0.0
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- yuvibim08 (7)
- JessicaP94 (3)
- apsuresh (1)
- Angeline-sys (1)
- CPUriarte (1)
- daniannr (1)
- lhollestein (1)
- Feng-Zhang (1)
- SGIlabes (1)
- ayhanxian (1)
- chujun225 (1)
- cathalgking (1)
- navern0net (1)
- Art-Ink (1)
- sgunz (1)
Pull Request Authors
- fuerzhou (18)
- Art-Ink (2)
- mblue9 (2)
- annatrigos (2)
- PeteHaitch (1)
- rubak (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 9,006 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 9
- Total maintainers: 1
bioconductor.org: SPIAT
Spatial Image Analysis of Tissues
- Homepage: https://trigosteam.github.io/SPIAT/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/SPIAT/inst/doc/SPIAT.pdf
- License: Artistic-2.0 + file LICENSE
-
Latest release: 1.10.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.2.0 depends
- SpatialExperiment * depends
- ComplexHeatmap * imports
- RANN >= 2.6.1 imports
- Rtsne * imports
- SummarizedExperiment * imports
- alphahull * imports
- apcluster >= 1.4.7 imports
- dbscan >= 1.1 imports
- dittoSeq * imports
- dplyr >= 0.8.3 imports
- elsa * imports
- ggplot2 >= 3.2.1 imports
- grDevices * imports
- graphics * imports
- gridExtra >= 2.3 imports
- gtools >= 3.8.1 imports
- methods * imports
- mmand >= 1.5.4 imports
- plotly >= 4.9.0 imports
- pracma >= 2.2.5 imports
- raster * imports
- reshape2 >= 1.4.3 imports
- rlang * imports
- sp * imports
- spatstat.core * imports
- spatstat.geom * imports
- stats * imports
- tibble >= 2.1.3 imports
- umap * imports
- utils * imports
- vroom * imports
- xROI * imports
- BiocStyle * suggests
- knitr * suggests
- pkgdown * suggests
- rmarkdown * suggests
- testthat * suggests
- JamesIves/github-pages-deploy-action v4.4.1 composite
- actions/checkout v3 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite