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:
Maintainer: Dharmesh D. Bhuva <dharmesh.bhuva at adelaide.edu.au>
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 | ||
| NEWS | Text |
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 |
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.
| Source Package | SpaNorm_1.1.0.tar.gz |
| Windows Binary (x86_64) | SpaNorm_1.1.0.zip |
| 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 |