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Bioconductor - SpaNorm (development version)

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 (3.22)

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: 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")): 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")
Details biocViews CellBiology, GeneExpression, Software, Spatial, Transcriptomics Version 1.3.0 In Bioconductor since BioC 3.20 (R-4.4) (0.5 years) 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 See More 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.

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