This is the development version of BatchSVG; for the stable release version, see BatchSVG.
Identify Batch-Biased Features in Spatially Variable GenesBioconductor version: Development (3.22)
`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 experiments, 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.
Author: Christine Hou [aut, cre] ORCID: 0009-0001-5350-0629 , Jacqui Thompson [aut], Stephanie C. Hicks [aut, fnd] ORCID: 0000-0002-7858-0231
Maintainer: Christine Hou <chris2018hou at gmail.com>
Citation (from within R, entercitation("BatchSVG")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("BatchSVG")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BatchSVG")Follow Installation instructions to use this package in your R session.
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