MoleculeExperiment
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 (3.24)
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("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 1.13.0, https://bioconductor.org/packages/MoleculeExperiment.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("MoleculeExperiment")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MoleculeExperiment")| "Introduction to MoleculeExperiment" | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, Software, Spatial, Transcriptomics |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | MIT + file LICENSE |
| 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 |
| System Requirements | |
| URL | https://github.com/SydneyBioX/MoleculeExperiment |
| Bug Reports | https://github.com/SydneyBioX/MoleculeExperiment/issues |
See More
| Suggests | knitr, BiocStyle, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MoleculeExperiment_1.13.0.tar.gz |
| Windows Binary (x86_64) | MoleculeExperiment_1.13.0.zip |
| macOS Binary (big-sur-x86_64) | MoleculeExperiment_1.13.0.tgz |
| macOS Binary (sonoma-arm64) | MoleculeExperiment_1.13.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MoleculeExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MoleculeExperiment |
| Package Short Url | https://bioconductor.org/packages/MoleculeExperiment/ |
| Package Downloads Report | Download Stats |