https://github.com/bioconductor-source/standr
Science Score: 36.0%
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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 -
○Academic email domains
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○Scientific vocabulary similarity
Low similarity (11.8%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- License: other
- Language: R
- Default Branch: devel
- Size: 8.11 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- 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: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
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Dependencies
- 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
- 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
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