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This is the development version of MoleculeExperiment; for the stable release version, see MoleculeExperiment.

Prioritising a molecule-level storage of Spatial Transcriptomics Data

Bioconductor version: Development (3.20)

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>

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


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

# The following initializes usage of Bioc devel


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Introduction to MoleculeExperiment HTML R Script
Reference Manual PDF


biocViews DataImport, DataRepresentation, Infrastructure, Software, Spatial, Transcriptomics
Version 1.5.1
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, stats
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