TENET.ExperimentHub
This is the development version of TENET.ExperimentHub; for the stable release version, see TENET.ExperimentHub.
Experiment data for the TENET package
Bioconductor version: Development (3.24)
ExperimentHub package containing datasets for use in the TENET package's vignette and function examples. These include a variety of different objects to illustrate different datasets used in TENET functions. Where applicable, all datasets are aligned to the hg38 human genome.
Author: Rhie Lab at the University of Southern California [cre], Daniel Mullen [aut]
, Zexun Wu [aut]
, Ethan Nelson-Moore [aut]
, Suhn Rhie [aut]
Maintainer: Rhie Lab at the University of Southern California <rhielab at gmail.com>
citation("TENET.ExperimentHub")):
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("TENET.ExperimentHub")
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("TENET.ExperimentHub")| Using the TENET.ExperimentHub datasets | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BreastCancerData, CancerData, CellCulture, ExperimentData, ExperimentHub, ExpressionData, Genome, Homo_sapiens_Data, MethylationArrayData, MicroarrayData, RNASeqData, Tissue |
| Version | 1.5.0 |
| License | GPL-2 |
| Depends | R (>= 4.5), ggplot2 (>= 4.0) |
| Imports | ExperimentHub, SummarizedExperiment, MultiAssayExperiment, GenomicRanges, methods |
| System Requirements | |
| URL | https://github.com/rhielab/TENET.ExperimentHub |
| Bug Reports | https://github.com/rhielab/TENET.ExperimentHub/issues |
See More
| Suggests | TENET, ExperimentHubData, testthat (>= 3.0.0), BiocManager, knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | TENET |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TENET.ExperimentHub_1.5.0.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/TENET.ExperimentHub |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TENET.ExperimentHub |
| Package Short Url | https://bioconductor.org/packages/TENET.ExperimentHub/ |
| Package Downloads Report | Download Stats |