SpaNorm
Spatially-aware normalisation for spatial transcriptomics data
Bioconductor version: 3.23 · Package version: 1.6.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SpaNorm")Details
| Maintainer | Dharmesh D. Bhuva <dharmesh.bhuva@adelaide.edu.au> |
| Author | Dharmesh D. Bhuva [aut, cre] (ORCID: <https://orcid.org/0000-0002-6398-9157>), Agus Salim [aut] (ORCID: <https://orcid.org/0000-0003-3999-7701>), Ahmed Mohamed [aut] (ORCID: <https://orcid.org/0000-0001-6507-5300>) |
| License | GPL (>= 3) |
| URL | https://bhuvad.github.io/SpaNorm |
| Bug Reports | https://github.com/bhuvad/SpaNorm/issues |
| Downloads rank | 416 |
| Source branch | RELEASE_3_23 |
| biocViews | CellBiology, GeneExpression, Software, Spatial, Transcriptomics |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SpaNorm_1.6.0.tar.gz |
| Windows binary (x86_64) | SpaNorm_1.6.0.zip |
| macOS binary (arm64) | SpaNorm_1.6.0.tgz |
| macOS binary (x86_64) | SpaNorm_1.6.0.tgz |
Dependencies
Depends: R (>= 4.4)
Imports: edgeR, ggplot2, Matrix, matrixStats, methods, rlang, scran, SeuratObject, SingleCellExperiment, SpatialExperiment, stats, SummarizedExperiment, S4Vectors, utils, BiocParallel, BiocSingular
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown, covr, BiocStyle, scater, Seurat (>= 5.0.0), patchwork, ggforce, ggnewscale, tensorflow