Package: SpaMTP
Type: Package
Title: Spatial Metabolomics and Multi-Omics Analysis
Version: 0.99.11
Authors@R: c(
    person("Andrew", "Causer",
            email = "a.causer@uq.edu.au", 
            role = c("aut"),
            comment = c(ORCID = "0009-0001-7341-8366")),
    person("Tianyao", "Lu",
            email = "lu.t@wehi.edu.au", 
            role = c("aut", "cre")),
    person("Christopher C.J.", "Fitzgerald",
            email = "cfitzgerald@marum.de",
            role = c("aut"),
            comment = c(ORCID = "0000-0003-3935-4300")),
    person("GML", "Lab",
            role = c("lbr")),
    person("Brain Cancer Research", "Lab",
            role = c("lbr")),
    person("UQ", "Institute",
            role = c("fnd")),
    person("QIMR", "Institute",
            role = c("fnd")),
    person("WEHI", "Institute",
            role = c("fnd"))
            )
Description: Provides analysis, annotation, visualisation, and
        multi-omic integration methods for spatial metabolomics data.
        SpaMTP interoperates with Cardinal and SpatialExperiment
        containers, with optional Seurat conversion; supports indexed
        accurate-mass annotation using versioned RaMP resources; and
        implements spatial feature analysis, pathway enrichment,
        pathway-network visualisation, and alignment with spatial
        transcriptomics data.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Suggests: BiocStyle, EnhancedVolcano, htmlTable, htmltools, kableExtra,
        knitr, patchwork, reticulate, rmarkdown, SeuratObject (>=
        5.0.0), SpaMTPData (>= 0.99.5), testthat (>= 3.0.0), viridis,
        yaml
Config/testthat/edition: 3
biocViews: MassSpectrometry, ImagingMassSpectrometry, Metabolomics,
        Spatial, Transcriptomics, Alignment
Imports: ape, BiocSingular, bluster, Cardinal, cowplot, data.table,
        digest, dplyr, DropletUtils, edgeR, fgsea, FNN, future,
        future.apply, ggdendro, ggplot2, ggridges, grDevices, graphics,
        grid, httr, htmlwidgets, jsonlite, limma, magick, magrittr,
        Matrix, mclust, methods, MSnbase, naturalsort, parallel,
        pheatmap, plotly, png, purrr, rgoslin, rlang, RSpectra, scales,
        scater, scran, sf, shiny, SingleCellExperiment, S4Vectors,
        SpaMTPdb (>= 0.99.4), SpatialExperiment, stats, stringr,
        SummarizedExperiment, tibble, tidyr, tools, utils, withr
URL: https://github.com/SpaMTP-project/SpaMTP,
        https://github.com/GenomicsMachineLearning/SpaMTP,
        https://genomicsmachinelearning.github.io/SpaMTP/,
        https://doi.org/10.1038/s41592-026-03140-8
BugReports: https://github.com/SpaMTP-project/SpaMTP/issues
Depends: R (>= 4.5.0)
VignetteBuilder: knitr
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev
        libglpk-dev make libmagick++-dev gsfonts libicu-dev libpng-dev
        libuv1-dev libxml2-dev libnetcdf-dev libssl-dev libproj-dev
        libsqlite3-dev libudunits2-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-14 00:22:44 UTC
RemoteUrl: https://github.com/BiocStaging/SpaMTP
RemoteRef: HEAD
RemoteSha: e320440d27a403758f04f2761d9f33d71bea9e81
NeedsCompilation: no
Packaged: 2026-10-14 02:16:17 UTC; root
Author: Andrew Causer [aut] (ORCID: <https://orcid.org/0009-0001-7341-8366>),
  Tianyao Lu [aut, cre],
  Christopher C.J. Fitzgerald [aut] (ORCID:
    <https://orcid.org/0000-0003-3935-4300>),
  GML Lab [lbr],
  Brain Cancer Research Lab [lbr],
  UQ Institute [fnd],
  QIMR Institute [fnd],
  WEHI Institute [fnd]
Maintainer: Tianyao Lu <lu.t@wehi.edu.au>