terraTCGAdata
This is the released version of terraTCGAdata; for the devel version, see terraTCGAdata.
OpenAccess TCGA Data on Terra as MultiAssayExperiment
Bioconductor version: Release (3.23)
Leverage the existing open access TCGA data on Terra with well-established Bioconductor infrastructure. Make use of the Terra data model without learning its complexities. With a few functions, you can copy / download and generate a MultiAssayExperiment from the TCGA example workspaces provided by Terra.
Author: Marcel Ramos [aut, cre]
Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>
citation("terraTCGAdata")):
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("terraTCGAdata")
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("terraTCGAdata")| Obtain Terra TCGA data as MultiAssayExperiment | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | Artistic-2.0 |
| Depends | AnVILGCP, MultiAssayExperiment |
| Imports | AnVIL, BiocFileCache, dplyr, GenomicRanges, methods, RaggedExperiment, readr, S4Vectors, stats, tidyr, TCGAutils, utils |
| System Requirements | |
| URL | https://github.com/waldronlab/terraTCGAdata |
| Bug Reports | https://github.com/waldronlab/terraTCGAdata/issues |
See More
| Suggests | AnVILBase, GCPtools, knitr, rmarkdown, BiocStyle, withr, 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 | terraTCGAdata_1.16.0.tar.gz |
| Windows Binary (x86_64) | terraTCGAdata_1.16.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | terraTCGAdata_1.16.0.tgz |
| macOS Binary (sonoma-arm64) | terraTCGAdata_1.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/terraTCGAdata |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/terraTCGAdata |
| Bioc Package Browser | https://code.bioconductor.org/browse/terraTCGAdata/ |
| Package Short Url | https://bioconductor.org/packages/terraTCGAdata/ |
| Package Downloads Report | Download Stats |