BatchSVG

Identify Batch-Biased Spatially Variable Genes

Bioconductor version: 3.23 · Package version: 1.4.0

BatchSVG is a method to identify batch-biased spatially variable genes (SVGs) in spatial transcriptomics data. The batch variable can be defined as sample, donor sex, or other batch effects of interest. The BatchSVG method is based on the binomial deviance model (Townes et al, 2019).

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BatchSVG")

Details

Maintainer	Kinnary Shah <kinnaryshahh@gmail.com>
Author	Christine Hou [aut] (ORCID: <https://orcid.org/0009-0001-5350-0629>), Kinnary Shah [aut, cre], Jacqueline R. Thompson [aut], Stephanie C. Hicks [aut, fnd] (ORCID: <https://orcid.org/0000-0002-7858-0231>)
License	Artistic-2.0
URL	https://github.com/christinehou11/BatchSVG, https://christinehou11.github.io/BatchSVG
Bug Reports	https://github.com/christinehou11/BatchSVG/issues
Downloads rank	282
Source branch	RELEASE_3_23
biocViews	BatchEffect, QualityControl, Software, Spatial, Transcriptomics

Documentation

Find Batch-biased SVGs

Download

Follow the installation instructions to use this package in your R session.

Source package	BatchSVG_1.4.0.tar.gz
Windows binary (x86_64)	BatchSVG_1.4.0.zip
macOS binary (arm64)	BatchSVG_1.4.0.tgz
macOS binary (x86_64)	BatchSVG_1.4.0.tgz

Dependencies

Depends: R (>= 4.5.0)

Imports: scry, dplyr, stats, rlang, cowplot, ggrepel, ggplot2, RColorBrewer, scales, SummarizedExperiment

Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, spatialLIBD