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
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.1%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: peicai
- Language: R
- Default Branch: main
- Homepage: https://peicai.github.io/DESpace/
- Size: 11 MB
Statistics
- Stars: 4
- Watchers: 1
- Forks: 1
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions
DESpace is a framework for identifying spatially variable genes (SVGs), a common task in spatial transcriptomics analyses, and differential spatial variable pattern (DSP) genes, which identify differences in spatial gene expression patterns across experimental conditions.
By leveraging pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression with a negative binomial (NB), via edgeR, with spatial clusters as covariates. SV genes are then identified by testing the significance of spatial clusters.
For multi-sample, multi-condition datasets, again we fit a NB model via edgeR, but this time we use spatial clusters, conditions and their interactions as covariates. DSP genes are then identified by testing the interaction between spatial clusters and conditions.
Check the vignettes for a description of the main conceptual and mathematical aspects, as well as usage guidelines.
Peiying Cai, Mark D. Robinson, and Simone Tiberi (2024).
DESpace: spatially variable gene detection via differential expression testing of spatial clusters.
Bioinformatics. Available here
Bioconductor installation
DESpace is available on Bioconductor and can be installed with the command:
r
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("DESpace")
Vignette
The vignette illustrating how to use the package can be accessed on
Bioconductor
or from R via:
r
vignette("DESpace")
or
r
browseVignettes("DESpace")
Owner
- Login: peicai
- Kind: user
- Repositories: 3
- Profile: https://github.com/peicai
GitHub Events
Total
- Issues event: 3
- Delete event: 2
- Issue comment event: 3
- Push event: 27
- Pull request event: 4
- Create event: 4
Last Year
- Issues event: 3
- Delete event: 2
- Issue comment event: 3
- Push event: 27
- Pull request event: 4
- Create event: 4
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 2
- Total pull requests: 7
- Average time to close issues: 17 minutes
- Average time to close pull requests: less than a minute
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 1.5
- Average comments per pull request: 0.0
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 4
- Average time to close issues: 17 minutes
- Average time to close pull requests: less than a minute
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 1.5
- Average comments per pull request: 0.0
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- lmweber (1)
- Antidington (1)
Pull Request Authors
- peicai (7)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 5,469 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: DESpace
DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions
- Homepage: https://github.com/peicai/DESpace https://peicai.github.io/DESpace/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/DESpace/inst/doc/DESpace.pdf
- License: GPL-3
-
Latest release: 2.0.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.3.0 depends
- BiocGenerics * imports
- BiocParallel * imports
- Matrix * imports
- S4Vectors * imports
- SpatialExperiment * imports
- SummarizedExperiment * imports
- assertthat * imports
- cowplot * imports
- data.table * imports
- dplyr * imports
- edgeR * imports
- ggforce * imports
- ggnewscale * imports
- ggplot2 * imports
- ggpubr * imports
- limma * imports
- methods * imports
- patchwork * imports
- scales * imports
- stats * imports
- BiocStyle * suggests
- ExperimentHub * suggests
- concaveman * suggests
- knitr * suggests
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- rmarkdown * suggests
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- spatialLIBD * suggests
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