Package: SpaNorm 1.7.4

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_1.7.4.tar.gz
SpaNorm_1.7.4.zip(r-4.7)SpaNorm_1.7.4.zip(r-4.6)SpaNorm_1.7.4.zip(r-4.5)
SpaNorm_1.7.4.tgz(r-4.6-any)SpaNorm_1.7.4.tgz(r-4.5-any)
SpaNorm_1.7.4.tar.gz(r-4.7-any)SpaNorm_1.7.4.tar.gz(r-4.6-any)
SpaNorm_1.7.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SpaNorm/json (API)

# 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-1.7.0(bioc 3.24)SpaNorm-1.6.0(bioc 3.23)

software geneexpression transcriptomics spatial cellbiology

6.58 score 18 stars 35 scripts 335 downloads 11 exports 106 dependencies

Last updated from:4319830ba3. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	223
linux-devel-x86_64	OK	604
source / vignettes	OK	555
linux-release-x86_64	OK	631
macos-release-arm64	OK	379
macos-oldrel-arm64	OK	366
windows-devel	OK	767
windows-release	OK	742
windows-oldrel	OK	771
wasm-release	OK	203

Exports:calculateMu fastSizeFactors filterGenes fitNB invert_mat 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

Rendered fromSpaNorm.Rmdusingknitr::rmarkdown

Last update: 2026-07-09
Started: 2024-05-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compute fitted means from a negative binomial GLM fit	calculateMu
Filter genes based on expression	fastSizeFactors fastSizeFactors,SpatialExperiment-method
Filter genes based on expression	filterGenes filterGenes,Seurat-method filterGenes,SpatialExperiment-method
Fit a per-gene negative binomial GLM	fitNB
Human dorsolateral prefrontal cortex (DLPFC) visium sample	HumanDLPFC
Invert a symmetric positive-definite matrix	invert_mat
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,Seurat-method SpaNormPCA,SpatialExperiment-method
Model-based spatially variable gene (SVG) calling	SpaNormSVG SpaNormSVG,Seurat-method SpaNormSVG,SpatialExperiment-method
Export top SVG results to a data frame	topSVGs