MouseAgingData
This is the development version of MouseAgingData; for the stable release version, see MouseAgingData.
Multi-omics data access for studies investigating the effects of aging
Bioconductor version: Development (3.24)
The MouseAgingData package provides analysis-ready data resources from different studies focused on aging and rejuvenation in mice. The package currently provides two 10x Genomics single-cell RNA-seq datasets. The first study profiled the aging mouse brain measured across 37,089 cells (Ximerakis et al., 2019). The second study investigated parabiosis by profiling a total of 105,329 cells (Ximerakis & Holton et al., 2023). The datasets are provided as SingleCellExperiment objects and provide raw UMI counts and cell metadata.
Author: Tram Nguyen [aut, cre]
, Kris Holton [aut], Tyrone Lee [aut], Nitesh Turaga [ctb], Ludwig Geistlinger [aut], Robert Gentleman [aut]
Maintainer: Tram Nguyen <tram22.nguyen at gmail.com>
citation("MouseAgingData")):
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("MouseAgingData")
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("MouseAgingData")| Accessing and Visualizing Parabiosis Droplet Data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, ExperimentHub, ExpressionData, Mus_musculus_Data, PackageTypeData, RNASeqData, SequencingData, SingleCellData |
| Version | 1.9.0 |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0), SingleCellExperiment |
| Imports | AnnotationHub, ExperimentHub |
| System Requirements | |
| URL | https://github.com/ccb-hms/MouseAgingData |
| Bug Reports | https://github.com/ccb-hms/MouseAgingData/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, scater |
| 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 | MouseAgingData_1.9.0.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/MouseAgingData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MouseAgingData |
| Package Short Url | https://bioconductor.org/packages/MouseAgingData/ |
| Package Downloads Report | Download Stats |