BatchSVG
Identification of biased features from SVGs in spatial transcriptomics data
Science Score: 26.0%
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Low similarity (7.2%) to scientific vocabulary
Keywords
Repository
Identification of biased features from SVGs in spatial transcriptomics data
Basic Info
- Host: GitHub
- Owner: christinehou11
- Language: R
- Default Branch: main
- Homepage: https://christinehou11.github.io/BatchSVG/
- Size: 15.5 MB
Statistics
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
BatchSVG
BatchSVG is a feature-based Quality Control (QC) to identify
SVGs on spatial transcriptomics data with specific types of batch effect.
Regarding to the spatial transcriptomics data experients, the batch can be
defined as "sample", "sex", and etc.The BatchSVG method is based on
binomial deviance model (Townes et al, 2019))
and applies cutoffs based on
the number of standard deviation (nSD) of relative change in deviance and
rank difference as the data-driven thresholding approach to detect the
batch-biased outliers.
Installation
BatchSVG is a R package available in Bioconductor version 3.19 and later.
You can install BatchSVG by using the following commands in R session from
Bioconductor.
``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") }
BiocManager::install("BatchSVG")
Check that you have a valid Bioconductor installation
BiocManager::valid() ```
The development version can be obtained by
r
BiocManager::install("christinehou11/BatchSVG")
Code of Conduct
Please note that the BatchSVG project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Owner
- Login: christinehou11
- Kind: user
- Repositories: 1
- Profile: https://github.com/christinehou11
GitHub Events
Total
- Watch event: 4
- Member event: 1
- Push event: 53
Last Year
- Watch event: 4
- Member event: 1
- Push event: 53
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 1,566 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 1
- Total maintainers: 1
bioconductor.org: BatchSVG
Identify Batch-Biased Features in Spatially Variable Genes
- Homepage: https://github.com/christinehou11/BatchSVG https://christinehou11.github.io/BatchSVG
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/BatchSVG/inst/doc/BatchSVG.pdf
- License: Artistic-2.0
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Latest release: 1.0.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.4.0 depends
- dplyr * depends
- tibble * depends
- RColorBrewer * imports
- SummarizedExperiment * imports
- ggplot2 * imports
- ggrepel * imports
- rlang * imports
- scry * imports
- stats * imports
- BiocStyle * suggests
- ExperimentHub * suggests
- SpatialExperiment * suggests
- humanHippocampus2024 * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests
- tidyr * suggests
- 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