SpaNorm

Spatially-aware normalisation for spatial transcriptomics data

Bioconductor version: 3.23 · Package version: 1.6.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SpaNorm")

Details

Maintainer	Dharmesh D. Bhuva <dharmesh.bhuva@adelaide.edu.au>
Author	Dharmesh D. Bhuva [aut, cre] (ORCID: <https://orcid.org/0000-0002-6398-9157>), Agus Salim [aut] (ORCID: <https://orcid.org/0000-0003-3999-7701>), Ahmed Mohamed [aut] (ORCID: <https://orcid.org/0000-0001-6507-5300>)
License	GPL (>= 3)
URL	https://bhuvad.github.io/SpaNorm
Bug Reports	https://github.com/bhuvad/SpaNorm/issues
Downloads rank	262
Source branch	RELEASE_3_23
biocViews	CellBiology, GeneExpression, Software, Spatial, Transcriptomics

Documentation

SpaNorm: Spatially aware library size normalisation

Download

Source package

Dependencies

Depends: R (>= 4.4)

Imports: edgeR, ggplot2, Matrix, matrixStats, methods, rlang, scran, SeuratObject, SingleCellExperiment, SpatialExperiment, stats, SummarizedExperiment, S4Vectors, utils, BiocParallel, BiocSingular

Suggests: testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown, covr, BiocStyle, scater, Seurat (>= 5.0.0), patchwork, ggforce, ggnewscale, tensorflow