SpaMTPData
This is the development version of SpaMTPData; to use it, please install the devel version of Bioconductor.
Experiment Data Resources for SpaMTP Workflows
Bioconductor version: Development (3.24)
Provides lightweight, version-aware access to spatial metabolomics and multi-omics experiment data used in SpaMTP workflows. Resources cover mouse brain, mouse urinary bladder, simulated single-cell multi-omics, annotation-refinement, and human brain examples. Large files are retrieved through ExperimentHub or verified source-URL caches rather than stored in the package repository. A small deterministic synthetic SpatialExperiment with a paired transcriptome supports offline examples and interoperability tests. Native SpatialExperiment datasets are available in a separate resource release; historical archival objects retain their original representations. Conversion and analysis are handled by the SpaMTP software package. Native experimental files share a Zenodo version family with SpaMTPdb without coupling the packages at runtime.
Author: Tianyao Lu [aut, cre], Andrew Causer [aut], Quan Nguyen [aut]
Maintainer: Tianyao Lu <lu.t at wehi.edu.au>
citation("SpaMTPData")):Tianyao Lu, Andrew Causer, Quan Nguyen. SpaMTPData: Experiment Data Resources for SpaMTP Workflows. doi:10.18129/B9.bioc.SpaMTPData, R package version 0.99.5, https://bioconductor.org/packages/SpaMTPData.
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("SpaMTPData")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("SpaMTPData")| Accessing SpaMTP Experiment Data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ExperimentData, ExperimentHub, Homo_sapiens_Data, Mus_musculus_Data, ReproducibleResearch |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | AnnotationHub, ExperimentHub, S4Vectors, SingleCellExperiment, SpatialExperiment, utils |
| System Requirements | |
| URL | https://github.com/BCRL-tylu/SpaMTPData |
| Bug Reports | https://github.com/BCRL-tylu/SpaMTPData/issues |
See More
| Suggests | BiocStyle, ExperimentHubData, jsonlite, knitr, rmarkdown, SummarizedExperiment, 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 | SpaMTPData_0.99.5.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/SpaMTPData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpaMTPData |
| Package Short Url | https://bioconductor.org/packages/SpaMTPData/ |
| Package Downloads Report | Download Stats |