Package: BatchSVG
Type: Package
Title: Identify Batch-Biased Spatially Variable Genes
Version: 1.3.2
Authors@R: 
    c(person(
        given = "Christine",
        family = "Hou",
        role = c("aut"),
        email = "chris2018hou@gmail.com",
        comment = c(ORCID = "0009-0001-5350-0629")
    ),
    c(person(
        given = "Kinnary",
        family = "Shah",
        role = c("aut", "cre"),
        email = "kinnaryshahh@gmail.com")
    ),    
    person(
        given = "Jacqui",
        family = "Thompson",
        role = "aut",
        email = "jthom338@jh.edu"
    ),
    person(
        given = "Stephanie C.", 
        family = "Hicks", 
        role = c("aut","fnd"),
        email = "shicks19@jhu.edu", 
        comment = c(ORCID = "0000-0002-7858-0231"))
    )
Description: `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](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1861-6))).
License: Artistic-2.0
Imports: scry, dplyr, stats, rlang, cowplot, ggrepel, ggplot2,
        RColorBrewer, scales, SummarizedExperiment
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: R (>= 4.5.0)
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, spatialLIBD
VignetteBuilder: knitr
biocViews: Spatial, Transcriptomics, BatchEffect, QualityControl
URL: https://github.com/christinehou11/BatchSVG,
        https://christinehou11.github.io/BatchSVG
BugReports: https://github.com/christinehou11/BatchSVG/issues
Config/testthat/edition: 3
LazyData: false
git_url: https://git.bioconductor.org/packages/BatchSVG
git_branch: devel
git_last_commit: 409e10b
git_last_commit_date: 2025-12-01
Repository: Bioconductor 3.23
Date/Publication: 2025-12-01
NeedsCompilation: no
Packaged: 2025-12-01 20:44:22 UTC; biocbuild
Author: Christine Hou [aut] (ORCID: <https://orcid.org/0009-0001-5350-0629>),
  Kinnary Shah [aut, cre],
  Jacqui Thompson [aut],
  Stephanie C. Hicks [aut, fnd] (ORCID:
    <https://orcid.org/0000-0002-7858-0231>)
Maintainer: Kinnary Shah <kinnaryshahh@gmail.com>
Built: R 4.6.0; ; 2025-12-02 04:33:00 UTC; unix
