Package: SpaNorm 1.5.2

Dharmesh D. Bhuva

SpaNorm: Spatially-aware normalisation for spatial transcriptomics data

This package implements the spatially aware library size normalisation algorithm, SpaNorm. SpaNorm normalises out library size effects while retaining biology through the modelling of smooth functions for each effect. Normalisation is performed in a gene- and cell-/spot- specific manner, yielding library size adjusted data.

Authors:Dharmesh D. Bhuva [aut, cre], Agus Salim [aut], Ahmed Mohamed [aut]

SpaNorm_1.5.2.tar.gz
SpaNorm_1.5.2.zip(r-4.6)SpaNorm_1.5.2.zip(r-4.5)
SpaNorm_1.5.2.tgz(r-4.6-any)SpaNorm_1.5.2.tgz(r-4.5-any)
SpaNorm_1.5.2.tar.gz(r-4.6-any)SpaNorm_1.5.2.tar.gz(r-4.5-any)
SpaNorm_1.5.2.tgz(r-4.5-emscripten)
SpaNorm.pdf |SpaNorm.html✨
SpaNorm/json (API)
NEWS

# Install 'SpaNorm' in R:

install.packages('SpaNorm', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bhuvad/spanorm/issues

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

Datasets:

HumanDLPFC - Human dorsolateral prefrontal cortex (DLPFC) visium sample

On BioConductor:SpaNorm-1.5.2(bioc 3.23)SpaNorm-1.4.0(bioc 3.22)

software geneexpression transcriptomics spatial cellbiology

6.61 score 17 stars 23 scripts 300 downloads 8 exports 106 dependencies

Last updated from:81ee46f8be. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	214
linux-devel-x86_64	NOTE	623
source / vignettes	OK	594
linux-release-x86_64	NOTE	625
macos-devel-arm64	NOTE	421
macos-release-arm64	NOTE	474
windows-devel	NOTE	952
windows-release	NOTE	927
wasm-release	OK	181

Exports:fastSizeFactors filterGenes plotCovariate plotSpatial SpaNorm SpaNormPCA SpaNormSVG topSVGs

Dependencies:abind askpass assorthead beachmat BH Biobase BiocFileCache BiocGenerics BiocNeighbors BiocParallel BiocSingular bit bit64 blob bluster cachem cli cluster codetools cpp11 curl DBI dbplyr DelayedArray digest dotCall64 dplyr dqrng edgeR farver fastmap filelock formatR futile.logger futile.options future future.apply generics GenomicRanges ggplot2 globals glue gtable httr2 igraph IRanges irlba isoband labeling lambda.r lattice lifecycle limma listenv locfit magick magrittr Matrix MatrixGenerics matrixStats memoise metapod openssl parallelly pillar pkgconfig progressr purrr R6 rappdirs RColorBrewer Rcpp RcppEigen rjson rlang RSQLite rsvd S4Arrays S4Vectors S7 ScaledMatrix scales scran scuttle Seqinfo SeuratObject SingleCellExperiment sitmo snow sp spam SparseArray SpatialExperiment statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector

SpaNorm: Spatially aware library size normalisation

Dharmesh D. Bhuva and Agus Salim

Rendered fromSpaNorm.Rmdusingknitr::rmarkdownon Mar 31 2026.

Last update: 2026-01-12
Started: 2024-05-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Filter genes based on expression	fastSizeFactors fastSizeFactors,SpatialExperiment-method
Filter genes based on expression	filterGenes filterGenes,Seurat-method filterGenes,SpatialExperiment-method
Human dorsolateral prefrontal cortex (DLPFC) visium sample	HumanDLPFC
Diagnostic plot of predicted expression for a covariate	plotCovariate
Plot spatial transcriptomic annotations per spot	plotSpatial
Spatially-dependent normalisation for spatial transcriptomics data	SpaNorm SpaNorm,Seurat-method SpaNorm,SpatialExperiment-method
An S4 class to store a SpaNorm model fit	$,SpaNormFit-method SpaNormFit SpaNormFit-class
GLM-based (SpaNorm) PCA	SpaNormPCA SpaNormPCA,SpatialExperiment-method
Model-based spatially variable gene (SVG) calling	SpaNormSVG SpaNormSVG,SpatialExperiment-method
Export top SVG results to a data frame	topSVGs