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")):
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")
## 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 |
| 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 |
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 |