MoleculeExperiment
This is the released version of MoleculeExperiment; for the devel version, see MoleculeExperiment.
Prioritising a molecule-level storage of Spatial Transcriptomics Data
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, Software, Spatial, Transcriptomics |
| Version | 1.12.0 |
| 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 |
Package Archives
Follow 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 (big-sur-x86_64) | MoleculeExperiment_1.12.0.tgz |
| macOS Binary (sonoma-arm64) | MoleculeExperiment_1.12.0.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 |