SpaNorm

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

Spatially-aware normalisation for spatial transcriptomics data

Bioconductor version: Development (3.21)

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: ), Agus Salim [aut] (ORCID: ), Ahmed Mohamed [aut] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
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	1.1.0
In Bioconductor since	BioC 3.20 (R-4.4) (< 6 months)
License	GPL (>= 3)
Depends	R (>= 4.4)
Imports	edgeR, ggplot2, Matrix, matrixStats, methods, rlang, scran, SeuratObject, SingleCellExperiment, SpatialExperiment, stats, SummarizedExperiment, S4Vectors, utils
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, Seurat, patchwork, ggforce, ggnewscale
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	SpaNorm_1.1.0.tar.gz
Windows Binary (x86_64)	SpaNorm_1.1.0.zip (64-bit only)
macOS Binary (x86_64)	SpaNorm_1.1.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/SpaNorm
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SpaNorm
Bioc Package Browser	https://code.bioconductor.org/browse/SpaNorm/
Package Short Url	https://bioconductor.org/packages/SpaNorm/
Package Downloads Report	Download Stats