Package: SpaNorm
Title: Spatially-aware normalisation for spatial transcriptomics data
Version: 1.7.4
Authors@R: c(
            person(given = "Dharmesh D.",
                   family = "Bhuva",
                   role = c("aut", "cre"),
                   email = "dharmesh.bhuva@adelaide.edu.au",
                   comment = c(ORCID = "0000-0002-6398-9157")),
            person(given = "Agus",
                   family = "Salim",
                   role = c("aut"),
                   email = "salim.a@unimelb.edu.au",
                   comment = c(ORCID = "0000-0003-3999-7701")),
            person(given = "Ahmed",
                   family = "Mohamed",
                   role = c("aut"),
                   email = "mohamed.a@wehi.edu.au",
                   comment = c(ORCID = "0000-0001-6507-5300"))
            )
Description: 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.
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
biocViews: Software, GeneExpression, Transcriptomics, Spatial,
        CellBiology
Depends: R (>= 4.4)
Imports: edgeR, ggplot2, Matrix, matrixStats, methods, rlang, scran,
        SeuratObject, SingleCellExperiment, SpatialExperiment, stats,
        SummarizedExperiment, S4Vectors, utils, BiocParallel,
        BiocSingular, DelayedArray
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown,
        covr, BiocStyle, scater, Seurat (>= 5.0.0), patchwork, ggforce,
        ggnewscale, torch
URL: https://bhuvad.github.io/SpaNorm
BugReports: https://github.com/bhuvad/SpaNorm/issues
VignetteBuilder: knitr
Config/testthat/edition: 3
LazyData: false
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libglpk-dev libmagick++-dev gsfonts libicu-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-11 06:19:48 UTC
RemoteUrl: https://github.com/bioc/SpaNorm
RemoteRef: HEAD
RemoteSha: 4319830ba3060212b917670296c4330b73a88766
NeedsCompilation: no
Packaged: 2026-07-11 15:47:24 UTC; root
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>)
Maintainer: Dharmesh D. Bhuva <dharmesh.bhuva@adelaide.edu.au>
Built: R 4.6.1; ; 2026-07-11 15:49:26 UTC; windows
