SpaNorm

This is the development version of SpaNorm; for the stable release version, see SpaNorm.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20

Spatially-aware normalisation for spatial transcriptomics data

Bioconductor version: Development (3.24)

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.

Author: Dharmesh D. Bhuva [aut, cre] ORCID: 0000-0002-6398-9157 , Agus Salim [aut] ORCID: 0000-0003-3999-7701 , Ahmed Mohamed [aut] ORCID: 0000-0001-6507-5300

Maintainer: Dharmesh D. Bhuva <dharmesh.bhuva at adelaide.edu.au>

Citation (from within R, enter citation("SpaNorm")):

Dharmesh D. Bhuva, Agus Salim, Ahmed Mohamed. SpaNorm: Spatially-aware normalisation for spatial transcriptomics data. doi:10.18129/B9.bioc.SpaNorm, R package version 1.7.4, https://bioconductor.org/packages/SpaNorm.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("SpaNorm")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SpaNorm")

SpaNorm	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBiology, GeneExpression, Software, Spatial, Transcriptomics
Version	1.7.4
In Bioconductor since	BioC 3.20 (R-4.4) (2 years)
License	GPL (>= 3)
Depends	R (>= 4.4)
Imports	edgeR, ggplot2, Matrix, matrixStats, methods, rlang, scran, SeuratObject, SingleCellExperiment, SpatialExperiment, stats, SummarizedExperiment, S4Vectors, utils, BiocParallel, BiocSingular, DelayedArray
System Requirements
URL	https://bhuvad.github.io/SpaNorm
Bug Reports	https://github.com/bhuvad/SpaNorm/issues

Suggests	testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown, covr, BiocStyle, scater, Seurat (>= 5.0.0), patchwork, ggforce, ggnewscale, torch
Linking To
Enhances
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Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SpaNorm_1.7.4.tar.gz
Windows Binary (x86_64)	SpaNorm_1.7.4.zip
macOS Binary (big-sur-x86_64)	SpaNorm_1.7.4.tgz
macOS Binary (sonoma-arm64)	SpaNorm_1.7.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SpaNorm
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SpaNorm
Package Short Url	https://bioconductor.org/packages/SpaNorm/
Package Downloads Report	Download Stats