MoleculeExperiment

Prioritising a molecule-level storage of Spatial Transcriptomics Data

Bioconductor version: Release (3.19)

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")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, Infrastructure, Software, Spatial, Transcriptomics
Version	1.4.1
In Bioconductor since	BioC 3.17 (R-4.3) (1.5 years)
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
System Requirements
URL	https://github.com/SydneyBioX/MoleculeExperiment
Bug Reports	https://github.com/SydneyBioX/MoleculeExperiment/issues

Suggests	knitr, BiocStyle, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MoleculeExperiment_1.4.1.tar.gz
Windows Binary (x86_64)	MoleculeExperiment_1.4.1.zip (64-bit only)
macOS Binary (x86_64)	MoleculeExperiment_1.4.1.tgz
macOS Binary (arm64)	MoleculeExperiment_1.4.1.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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.19	Source Archive