R-based User-Friendly Spatial Metabolomic, Transcriptomic, and Proteomic Data Analysis Tool
SpaMTP is an R package designed for the integrative analysis of spatial metabolomics and spatial transcriptomics data. SpaMTP inherits functionalities from two well established R packages (Cardinal and Seurat) to present a user-friendly platform for integrative spatial-omics analysis. Build on the foundation of a Seurat Class Object, this package has three major functionalities which include; (1) mass-to-charge ratio (m/z) metabolite annotation, (2) various downstream statistical analysis including differential metabolite expression and pathway analysis, and (3) integrative spatial-omics analysis. In addition, this package includes various functions for data visualisation and data import/export, permitting flexible usage with other established R and Python packages.
For more information and citing SpaMTP please visit our pre-print available here.
Installation
You can install the current version of SpaMTP from GitHub with:
if (!require("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github("GenomicsMachineLearning/SpaMTP")For tutorials and more information please visit the SpaMTP website