SpaNorm

This is the released version of SpaNorm; for the devel version, see SpaNorm.

Spatially-aware normalisation for spatial transcriptomics data

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DOI: 10.18129/B9.bioc.SpaNorm

Bioconductor version: Release (3.22)

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 iD ORCID: 0000-0002-6398-9157 , Agus Salim [aut] ORCID iD ORCID: 0000-0003-3999-7701 , Ahmed Mohamed [aut] ORCID iD ORCID: 0000-0001-6507-5300

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")
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 1.4.0

In Bioconductor since BioC 3.20 (R-4.4) (1 year)

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

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Package Archives

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

Source Package SpaNorm_1.4.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) SpaNorm_1.4.0.tgz

macOS Binary (arm64) SpaNorm_1.4.0.tgz

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/

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