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Prioritising a molecule-level storage of Spatial Transcriptomics Data

Bioconductor version: Release (3.18)

MoleculeExperiment contains functions to create and work with objects from the new MoleculeExperiment class. We introduce this class for analysing molecule-based spatial transcriptomics data (e.g., Xenium by 10X, Cosmx SMI by Nanostring, and Merscope by Vizgen). This allows researchers to analyse spatial transcriptomics data at the molecule level, and to have standardised data formats accross vendors.

Author: Bárbara Zita Peters Couto [aut], Nicholas Robertson [aut], Ellis Patrick [aut], Shila Ghazanfar [aut, cre]

Maintainer: Shila Ghazanfar <shazanfar at gmail.com>

Citation (from within R, enter citation("MoleculeExperiment")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to MoleculeExperiment HTML R Script
Reference Manual PDF


biocViews DataImport, DataRepresentation, Infrastructure, Software, Spatial, Transcriptomics
Version 1.2.2
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License MIT + file LICENSE
Depends R (>= 2.10)
Imports SpatialExperiment, Matrix, purrr, data.table, dplyr (>= 1.1.1), magrittr, rjson, utils, methods, terra, ggplot2, rlang, cli, EBImage, rhdf5, BiocParallel, S4Vectors
System Requirements
URL https://github.com/SydneyBioX/MoleculeExperiment
Bug Reports https://github.com/SydneyBioX/MoleculeExperiment/issues
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Suggests knitr, BiocStyle, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package MoleculeExperiment_1.2.2.tar.gz
Windows Binary MoleculeExperiment_1.2.2.zip
macOS Binary (x86_64) MoleculeExperiment_1.2.2.tgz
macOS Binary (arm64) MoleculeExperiment_1.2.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/MoleculeExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MoleculeExperiment
Bioc Package Browser https://code.bioconductor.org/browse/MoleculeExperiment/
Package Short Url https://bioconductor.org/packages/MoleculeExperiment/
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Old Source Packages for BioC 3.18 Source Archive