Package: BatchSVG 1.4.0

Kinnary Shah

BatchSVG: Identify Batch-Biased Spatially Variable Genes

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).

Authors:Christine Hou [aut], Kinnary Shah [aut, cre], Jacqueline R. Thompson [aut], Stephanie C. Hicks [aut, fnd]

BatchSVG_1.4.0.tar.gz
BatchSVG_1.4.0.zip(r-4.7)BatchSVG_1.4.0.zip(r-4.6)BatchSVG_1.4.0.zip(r-4.5)
BatchSVG_1.4.0.tgz(r-4.6-any)BatchSVG_1.4.0.tgz(r-4.5-any)
BatchSVG_1.4.0.tar.gz(r-4.7-any)BatchSVG_1.4.0.tar.gz(r-4.6-any)
BatchSVG_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
BatchSVG/json (API)
NEWS

# Install 'BatchSVG' in R:
install.packages('BatchSVG', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/christinehou11/batchsvg/issues

Pkgdown/docs site:https://christinehou11.github.io

Datasets:
  • list_batch_df - List of data frames of nSD(s) on the batch of subject

On BioConductor:BatchSVG-1.5.3(bioc 3.24)BatchSVG-1.4.0(bioc 3.23)

spatialtranscriptomicsbatcheffectqualitycontrolbatch-effectbioconductor-packagespatial-transcriptomics

5.14 score 3 stars 13 scripts 3 exports 62 dependencies

Last updated from:402c3bd7e3 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE286
linux-devel-x86_64OK595
source / vignettesOK555
linux-release-x86_64OK587
macos-release-arm64OK625
macos-oldrel-arm64OK627
windows-develOK1888
windows-releaseOK2090
windows-oldrelOK1860
wasm-releaseOK231

Exports:biasDetectfeatureSelectsvg_nSD

Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsBiocParallelBiocSingularclicodetoolscowplotcpp11DelayedArraydplyrfarverformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggrepelglmpcagluegtableIRangesirlbaisobandlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatspillarpkgconfigR6RColorBrewerRcpprlangrsvdS4ArraysS4VectorsS7ScaledMatrixscalesscrySeqinfoSingleCellExperimentsnowSparseArraySummarizedExperimenttibbletidyselectutf8vctrsviridisLitewithrXVector

Find Batch-biased SVGs

Kinnary Shah, Christine Hou

Rendered fromspe.Rmdusingknitr::rmarkdownon Jun 16 2026.

Last update: 2025-12-01
Started: 2024-10-19