MoleculeExperiment

The goal of MoleculeExperiment is to provide functionality for the representation and summarisation of imaging-based spatial transcriptomics data, including 10X Xenium.

MoleculeExperiment will take you from machine output data directly to an object ready for analyses! 🚀

We used the following data bundles to inform our readXenium, readCosmx and readMerscope functions respectively. In particular, Xenium data corresponds to 3 replicates from fresh frozen mouse brain tissue, accessed on 8 February 2023; CosMx data corresponds to human non-small cell lung cancer accessed on 27 February 2023; and MERSCOPE data is from human ovarian cancer accessed on 27 February 2023.

Installation

You can install the development version of MoleculeExperiment from GitHub with:

# install.packages("devtools")
devtools::install_github("SydneyBioX/MoleculeExperiment")

System dependencies

Note that the following 3 system dependencies are required: * libssl-dev * libmagick++-dev * libgdal-dev

Citation

Peters Couto et al, 2023, Bioinformatics