Package: BatchSVG 1.5.3

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_1.5.3.tar.gz
BatchSVG_1.5.3.zip(r-4.7)BatchSVG_1.5.3.zip(r-4.6)BatchSVG_1.5.3.zip(r-4.5)
BatchSVG_1.5.3.tgz(r-4.6-any)BatchSVG_1.5.3.tgz(r-4.5-any)
BatchSVG_1.5.3.tar.gz(r-4.7-any)BatchSVG_1.5.3.tar.gz(r-4.6-any)
BatchSVG_1.5.3.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.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-1.5.2(bioc 3.24)BatchSVG-1.4.0(bioc 3.23)

spatialtranscriptomicsbatcheffectqualitycontrolbatch-effectbioconductor-packagespatial-transcriptomics

5.24 score 3 stars 13 scripts 269 downloads 3 exports 62 dependencies

Last updated from:e95b4dd91a. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE281
linux-devel-x86_64OK646
source / vignettesOK423
linux-release-x86_64OK595
macos-release-arm64OK514
macos-oldrel-arm64OK639
windows-develOK1810
windows-releaseOK2009
windows-oldrelOK1700
wasm-releaseOK263

Exports:biasDetectfeatureSelectsvg_nSD

Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsBiocParallelBiocSingularclicodetoolscowplotcpp11DelayedArraydplyrfarverformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggrepelglmpcagluegtableIRangesirlbaisobandlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatspillarpkgconfigR6RColorBrewerRcpprlangrsvdS4ArraysS4VectorsS7ScaledMatrixscalesscrySeqinfoSingleCellExperimentsnowSparseArraySummarizedExperimenttibbletidyselectutf8vctrsviridisLitewithrXVector

Find Batch-biased SVGs

Kinnary Shah, Christine Hou

Rendered fromspe.Rmdusingknitr::rmarkdownon Jun 10 2026.

Last update: 2026-06-10
Started: 2024-10-19