MoleculeExperiment
Prioritising a molecule-level storage of Spatial Transcriptomics Data
Bioconductor version: 3.23 · Package version: 1.12.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MoleculeExperiment")Details
| Maintainer | Shila Ghazanfar <shazanfar@gmail.com> |
| Author | Bárbara Zita Peters Couto [aut], Nicholas Robertson [aut], Ellis Patrick [aut], Shila Ghazanfar [aut, cre] |
| License | MIT + file LICENSE |
| URL | https://github.com/SydneyBioX/MoleculeExperiment |
| Bug Reports | https://github.com/SydneyBioX/MoleculeExperiment/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, DataRepresentation, Infrastructure, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/MoleculeExperiment/ |
Citation
From within R, enter citation("MoleculeExperiment"):
Bárbara Zita Peters Couto, Nicholas Robertson, Ellis Patrick, Shila Ghazanfar. MoleculeExperiment: Prioritising a molecule-level storage of Spatial Transcriptomics Data. doi:10.18129/B9.bioc.MoleculeExperiment, R package version 1.12.0, https://bioconductor.org/packages/MoleculeExperiment.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | MoleculeExperiment_1.12.0.tar.gz |
| Windows binary (x86_64) | MoleculeExperiment_1.12.0.zip |
| macOS binary (arm64) | MoleculeExperiment_1.12.0.tgz |
| macOS binary (x86_64) | MoleculeExperiment_1.12.0.tgz |
Dependencies
Depends: R (>= 4.1.0)
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)