SpaNorm
R package for normalisation of spatial transcriptomics data
Science Score: 36.0%
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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
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○Academic publication links
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✓Committers with academic emails
4 of 5 committers (80.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.3%) to scientific vocabulary
Keywords from Contributors
Repository
R package for normalisation of spatial transcriptomics data
Basic Info
- Host: GitHub
- Owner: bhuvad
- License: gpl-3.0
- Language: R
- Default Branch: master
- Homepage: https://bhuvad.github.io/SpaNorm/
- Size: 96.4 MB
Statistics
- Stars: 13
- Watchers: 3
- Forks: 2
- Open Issues: 3
- Releases: 0
Metadata Files
README.md
SpaNorm - Spatially-aware normalisation for spatial transcriptomics data
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SpaNorm is a spatially aware library size normalisation method that removes library size effects, while retaining biology. Library sizes need to be removed from molecular datasets to allow comparisons across observations, in this case, across space. Bhuva et al. (2024) and Atta et al. (2023) have shown that standard single-cell inspired library size normalisation approaches are not appropriate for spatial molecular datasets as they often remove biological signals while doing so. This is because library size confounds biology in spatial molecular data.
SpaNorm uses a unique approach to spatially constraint modelling approach to model gene expression (e.g., counts) and remove library size effects, while retaining biology. It achieves this through three key innovations:
- Computing spatially smooth functions (using thin plate splines) to represent the gene- and location-/cell-/spot- specific size factors.
- Optimal decomposition of spatial variation into spatially smooth library size associated (technical) and library size independent (biology) variation using generalized linear models (GLMs).
- Adjustment of data using percentile adjusted counts (PAC) (Salim et al., 2022), as well as other adjustment approaches (e.g., Pearson).
Installation
SpaNorm can be installed from Bioconductor directly as follows:
``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("SpaNorm") ```
The development version can be installed as follows:
``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("bhuvad/SpaNorm") ```
Owner
- Name: Dharmesh Bhuva
- Login: bhuvad
- Kind: user
- Location: Adelaide
- Company: University of Adelaide
- Twitter: bhuva_dd
- Repositories: 2
- Profile: https://github.com/bhuvad
Post-doc working on systems biology and spatial statistics.
GitHub Events
Total
- Issues event: 7
- Watch event: 2
- Issue comment event: 9
- Push event: 41
- Create event: 2
Last Year
- Issues event: 7
- Watch event: 2
- Issue comment event: 9
- Push event: 41
- Create event: 2
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Dharmesh Bhuva | d****a@a****u | 90 |
| Agus Salim | l****g@g****m | 11 |
| bhuvad | d****a@u****u | 5 |
| A Wokaty | a****y@s****u | 2 |
| J Wokaty | j****y@s****u | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 6
- Total pull requests: 0
- Average time to close issues: 3 months
- Average time to close pull requests: N/A
- Total issue authors: 6
- Total pull request authors: 0
- Average comments per issue: 1.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 0
- Average time to close issues: 3 months
- Average time to close pull requests: N/A
- Issue authors: 6
- Pull request authors: 0
- Average comments per issue: 1.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- aelhossiny (1)
- swaruplab (1)
- Lahiru-lsb (1)
- Jorges1000 (1)
- mjemons (1)
- jordan841220 (1)
- marcouderzo (1)
- ashsolano (1)
- erikgerdtsson (1)
- roanvanscheppingen (1)
Pull Request Authors
- joaolsf (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 2,516 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
bioconductor.org: SpaNorm
Spatially-aware normalisation for spatial transcriptomics data
- Homepage: https://bhuvad.github.io/SpaNorm
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/SpaNorm/inst/doc/SpaNorm.pdf
- License: GPL (>= 3)
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Latest release: 1.2.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.2.0 depends
- Matrix >=1.2 imports
- MultipleExperiment >= 0.99.0 imports
- SingleCellExperiment >= 1.14.1 imports
- SpatialExperiment >= 1.8.1 imports
- SummarizedExperiment >= 1.28.0 imports
- edgeR >= 3.34.0 imports
- matrixStats >= 0.63.0 imports
- scater >= 1.26.1 imports
- scran >= 1.26.2 imports
- knitr * suggests
- rmarkdown * suggests
- actions/checkout v4 composite
- r-lib/actions/check-r-package v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- JamesIves/github-pages-deploy-action v4.5.0 composite
- actions/checkout v4 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- bioconductor/bioconductor_docker RELEASE_3_19 build