Package: BatchSVG
Type: Package
Title: Identify Batch-Biased Features in Spatially Variable Genes
Version: 1.1.1
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 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.
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: 90398e8
git_last_commit_date: 2025-10-06
Repository: Bioconductor 3.22
Date/Publication: 2025-10-07
NeedsCompilation: no
Packaged: 2025-10-07 19:43:37 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 4.5.1; ; 2025-10-08 02:37:19 UTC; unix
