Package: BatchSVG
Type: Package
Title: Identify Batch-Biased Features in Spatially Variable Genes
Version: 1.2.0
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 (>= 4.4.0)
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
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:36:00 UTC
RemoteUrl: https://github.com/bioc/BatchSVG
RemoteRef: RELEASE_3_22
RemoteSha: 9593ada3b1dfaaeb1fdc82487bcf7a4402727a0f
NeedsCompilation: no
Packaged: 2025-11-11 13:20:43 UTC; root
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 4.5.2; ; 2025-11-11 13:27:15 UTC; windows
