Science Score: 54.0%
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 3 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org -
✓Committers with academic emails
4 of 8 committers (50.0%) from academic institutions -
✓Institutional organization owner
Organization davislaboratory has institutional domain (www.wehi.edu.au) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.8%) to scientific vocabulary
Keywords from Contributors
Repository
Spatial transcriptomics analyses and decoding in R
Basic Info
- Host: GitHub
- Owner: DavisLaboratory
- License: other
- Language: R
- Default Branch: devel
- Homepage: https://davislaboratory.github.io/standR/
- Size: 34.3 MB
Statistics
- Stars: 22
- Watchers: 3
- Forks: 4
- Open Issues: 8
- Releases: 0
Metadata Files
README.md
standR: spatial transcriptomics analyses and decoding in R 
The standR package provides a series of functions to assist different stages of the analysis of spatial transcriptomics data generated from the Nanostring's GeoMX DSP platforms. Most functions in the package is based on the infrastructure SpatialExperiment, see detials here.
See full guide at HERE
Overall workflow
Example data
The published GeoMX WTA data of diabetic kidney disease that we used in the vignette is available here.
Installation
Install the release version from Bioconductor
``` if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("standR") ```
Install development version from GitHub
library(devtools)
devtools::install_github("DavisLaboratory/standR")
Citation
To cite standR, plese cite the following article: https://doi.org/10.1093/nar/gkad1026 Much appreciated!
Owner
- Name: Davis Laboratory
- Login: DavisLaboratory
- Kind: organization
- Location: Melbourne, Australia
- Website: http://www.wehi.edu.au/people/melissa-davis
- Repositories: 18
- Profile: https://github.com/DavisLaboratory
computational systems biology of cancer
GitHub Events
Total
- Issues event: 17
- Watch event: 3
- Issue comment event: 17
- Push event: 2
Last Year
- Issues event: 17
- Watch event: 3
- Issue comment event: 17
- Push event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| ningbioinfostruggling | l****n@w****u | 192 |
| Ahmed Mohamed | m****d@k****p | 34 |
| bhuva.d | b****d@w****u | 9 |
| J Wokaty | j****y | 4 |
| J Wokaty | j****y@s****u | 2 |
| Nitesh Turaga | n****a@g****m | 2 |
| Roy Lardenoije | 3****e | 2 |
| kieranrcampbell | k****l@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 39
- Total pull requests: 8
- Average time to close issues: 4 months
- Average time to close pull requests: 16 days
- Total issue authors: 34
- Total pull request authors: 5
- Average comments per issue: 1.46
- Average comments per pull request: 0.5
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 8
- Pull requests: 0
- Average time to close issues: 9 months
- Average time to close pull requests: N/A
- Issue authors: 8
- Pull request authors: 0
- Average comments per issue: 0.63
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ningbioinfo (4)
- jheonsuh (2)
- Sigmatilde (2)
- jjoo12 (1)
- bl24 (1)
- jaredmcollette (1)
- ErickMUO (1)
- knadia07 (1)
- kav-ita (1)
- JoanCG (1)
- cjstepek (1)
- LPotter21 (1)
- inijman (1)
- iddryg (1)
- ChelseaCHENX (1)
Pull Request Authors
- ningbioinfo (4)
- dkcoxie (2)
- kieranrcampbell (1)
- bhuvad (1)
- lardenoije (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 9,320 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: standR
Spatial transcriptome analyses of Nanostring's DSP data in R
- Homepage: https://github.com/DavisLaboratory/standR
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/standR/inst/doc/standR.pdf
- License: MIT + file LICENSE
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Latest release: 1.12.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.1 depends
- Biobase * imports
- BiocGenerics * imports
- RUVSeq * imports
- S4Vectors * imports
- SingleCellExperiment * imports
- SpatialExperiment >= 1.5.2 imports
- SummarizedExperiment * imports
- dplyr * imports
- edgeR * imports
- ggalluvial * imports
- ggplot2 * imports
- grDevices * imports
- limma * imports
- mclustcomp * imports
- methods * imports
- patchwork * imports
- readr * imports
- rlang * imports
- ruv * imports
- stats * imports
- tibble * imports
- tidyr * imports
- ExperimentHub * suggests
- cluster * suggests
- ggpubr * suggests
- ggrepel * suggests
- knitr * suggests
- rmarkdown * suggests
- scater * suggests
- testthat >= 3.0.0 suggests
- uwot * suggests
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- docker/build-push-action v1 composite
- r-lib/actions/setup-pandoc v2-branch composite
- r-lib/actions/setup-r v2-branch composite