Science Score: 23.0%
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
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○Academic publication links
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✓Committers with academic emails
3 of 7 committers (42.9%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.7%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
From geospatial to spatial -omics
Basic Info
- Host: GitHub
- Owner: pachterlab
- License: artistic-2.0
- Language: R
- Default Branch: main
- Homepage: https://pachterlab.github.io/voyager/
- Size: 4.33 GB
Statistics
- Stars: 95
- Watchers: 4
- Forks: 13
- Open Issues: 21
- Releases: 0
Topics
Metadata Files
README.md
From geospatial to spatial transcriptomics
<!-- badges: end -->
This package brings the tradition of geospatial statistics to spatial omics by wrapping classical geospatial packages such as spdep and gstat to be used with the SpatialFeatureExperiment class, which extends SpatialExperiment with sf.
The companion website for this package includes vignettes that showcase the functionality of Voyager in the context of the Visium, Slide-seq V2, CosMx, Xenium, and MERFISH technologies.
Installation
This package is in Bioconductor version 3.16 and above. Install with
r
if (!requireNamespace("BiocManager")) install.packages("BiocManager")
BiocManager::install(version = "3.17") # Or a higher version in the future
BiocManager::install("Voyager")
The main branch in this repo is the release version. The development version of Voyager can be installed from GitHub with:
```r
install.packages("remotes")
remotes::install_github("pachterlab/voyager", ref = "devel") ```
Or from Bioconductor with:
r
BiocManager::install("Voyager", version = "devel")
For contributors
The whole git repo of this package is huge because of the large number of figures and Jupyter notebooks in the documentation website. To reduce download time and disk space usage, you may clone the devel branch only, so the documentation branches are not cloned:
git clone -b devel --single-branch https://github.com/pachterlab/voyager.git
Owner
- Name: Pachter Lab
- Login: pachterlab
- Kind: organization
- Email: lpachter@caltech.edu
- Location: Pasadena, CA
- Website: http://pachterlab.github.io
- Repositories: 128
- Profile: https://github.com/pachterlab
GitHub Events
Total
- Issues event: 21
- Watch event: 22
- Issue comment event: 27
- Push event: 96
- Fork event: 3
Last Year
- Issues event: 21
- Watch event: 22
- Issue comment event: 27
- Push event: 96
- Fork event: 3
Committers
Last synced: 11 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Lambda Moses | d****2@c****u | 399 |
| J Wokaty | j****y@s****u | 10 |
| Kayla Jackson | 3****n | 4 |
| Lior Pachter | l****r@g****m | 3 |
| Laura Luebbert | 5****t | 1 |
| alikhuseynov | a****v@g****m | 1 |
| Kayla Jackson | k****n@c****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 52
- Total pull requests: 1
- Average time to close issues: 2 months
- Average time to close pull requests: less than a minute
- Total issue authors: 16
- Total pull request authors: 1
- Average comments per issue: 1.9
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 16
- Pull requests: 0
- Average time to close issues: 11 days
- Average time to close pull requests: N/A
- Issue authors: 10
- Pull request authors: 0
- Average comments per issue: 1.19
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- lambdamoses (29)
- alikhuseynov (4)
- huiyijiangling (4)
- heziqing (2)
- rsbivand (2)
- abadgerw (1)
- wudustan (1)
- ccruizm (1)
- chrkuo (1)
- Elena983 (1)
- cstrlln (1)
- spcdot (1)
- MohammadFaizIqbalFaiz (1)
- swbioinf (1)
- vraghu90 (1)
Pull Request Authors
- lambdamoses (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- R >= 4.2.0 depends
- BiocParallel * imports
- Matrix * imports
- S4Vectors * imports
- SingleCellExperiment * imports
- SpatialExperiment * imports
- SpatialFeatureExperiment * imports
- SummarizedExperiment * imports
- bluster * imports
- ggnewscale * imports
- ggplot2 * imports
- methods * imports
- patchwork * imports
- scales * imports
- scico * imports
- sf * imports
- spdep * imports
- stats * imports
- BiocSingular * suggests
- BiocStyle * suggests
- ExperimentHub * suggests
- SFEData * suggests
- cowplot * suggests
- knitr * suggests
- rmarkdown * suggests
- scater * suggests
- scran * suggests
- sparseMatrixStats * suggests
- testthat >= 3.0.0 suggests
- vdiffr * suggests
- JamesIves/github-pages-deploy-action 4.1.4 composite
- actions/checkout v2 composite
- grimbough/bioc-actions/setup-bioc v1 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- JamesIves/github-pages-deploy-action 4.1.4 composite
- actions/checkout v2 composite
- grimbough/bioc-actions/setup-bioc v1 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- actions/checkout v2 composite
- grimbough/bioc-actions/setup-bioc v1 composite
- r-lib/actions/setup-r-dependencies v2 composite