Package: MoleculeExperiment Title: Prioritising a molecule-level storage of Spatial Transcriptomics Data Version: 1.13.0 Authors@R: c( person("Bárbara Zita", "Peters Couto", email = "barbara.zita.peters@couto.de", role = c("aut")), person("Nicholas","Robertson", email = "nicholas.robertson@sydney.edu.au", role = c("aut")), person("Ellis", "Patrick", email = "ellis.patrick@sydney.edu.au", role = c("aut")), person("Shila", "Ghazanfar", email = "shazanfar@gmail.com", role = c("aut", "cre"))) Description: 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. License: MIT + file LICENSE Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 7.3.1 URL: https://github.com/SydneyBioX/MoleculeExperiment BugReports: https://github.com/SydneyBioX/MoleculeExperiment/issues Imports: SpatialExperiment, Matrix, purrr, data.table, dplyr (>= 1.1.1), magrittr, rjson, utils, methods, terra, ggplot2, rlang, cli, EBImage, rhdf5, BiocParallel, S4Vectors, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) VignetteBuilder: knitr biocViews: DataImport, DataRepresentation, Infrastructure, Software, Spatial, Transcriptomics Config/testthat/edition: 3 Depends: R (>= 4.1.0) Config/pak/sysreqs: cmake libfftw3-dev libgdal-dev gdal-bin libgeos-dev make libmagick++-dev gsfonts libicu-dev libjpeg-dev libpng-dev libtiff-dev libuv1-dev libssl-dev libproj-dev libsqlite3-dev zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 13:00:36 UTC RemoteUrl: https://github.com/bioc/MoleculeExperiment RemoteRef: HEAD RemoteSha: 1b1963e54c2b98c34b8de18cb3684db17f212980 NeedsCompilation: no Packaged: 2026-07-03 14:46:34 UTC; root Author: Bárbara Zita Peters Couto [aut], Nicholas Robertson [aut], Ellis Patrick [aut], Shila Ghazanfar [aut, cre] Maintainer: Shila Ghazanfar