Package: SpaMTP

Type: Package

Title: User Friendly Spatial Metabolomic Data Analysis Package

Version: 1.1.0.9000

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"))

)

Maintainer: Tianyao Lu <lu.t@wehi.edu.au>

Description: This is an easy-to-use spatial metabolomic data analysis package that harnesses the functionality of Cardinal and Seurat. In addition to easier and quicker plotting, this package contains additional function for various downstream analyses such as differential peak analysis, merging of Metabolomic and Spatial Transcriptomic (Visium) data, m/z metabolite annotation, and others. SpaMTP is maintained by Tianyao Lu.

License: MIT + file LICENSE

Encoding: UTF-8

Roxygen: list(markdown = TRUE)

RoxygenNote: 7.3.3

Suggests:

ape,

digest,

EnhancedVolcano,

htmlTable,

htmltools,

kableExtra,

knitr,

mclust,

patchwork,

reticulate,

rmarkdown,

testthat (>= 3.0.0),

viridis,

yaml

Config/testthat/edition: 3

biocViews:

Imports:

Cardinal,

cowplot,

data.table,

dplyr,

DropletUtils,

EBImage,

edgeR,

fgsea,

fields,

FNN,

future,

future.apply,

ggdendro,

ggnewscale,

ggplot2,

ggridges,

grDevices,

grid,

httr,

igraph,

jsonlite,

limma,

magick,

magrittr,

Matrix,

matter,

methods,

MSnbase,

naturalsort,

pbapply,

pheatmap,

plotly,

png,

purrr,

RColorBrewer,

rgoslin,

rlang,

RSpectra,

scales,

scater,

Seurat,

SeuratObject,

sf,

shiny,

shinyjs,

SingleCellExperiment,

stringr,

tibble,

tidyr,

utils,

zeallot

URL: https://github.com/genomicsmachinelearning/SpaMTP, https://genomicsmachinelearning.github.io/SpaMTP, https://genomicsmachinelearning.github.io/SpaMTP/developmental, https://doi.org/10.1038/s41592-026-03140-8

BugReports: https://github.com/genomicsmachinelearning/SpaMTP/issues

Depends:

R (>= 3.5)

LazyData: true

LazyDataCompression: xz

VignetteBuilder: knitr