curatedTCGAData
This is the released version of curatedTCGAData; for the devel version, see curatedTCGAData.
Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
Bioconductor version: Release (3.23)
This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment.
Author: Marcel Ramos [aut, cre]
, Levi Waldron [ctb], Lucas Schiffer [ctb], Ludwig Geistlinger [ctb], Valerie Obenchain [ctb], Martin Morgan [ctb], NCI [fnd] (GrantNo.: U24CA289073)
Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>
citation("curatedTCGAData")):
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("curatedTCGAData")
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("curatedTCGAData")| curatedTCGAData | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CancerData, ExperimentData, ExperimentHub, Homo_sapiens_Data, ReproducibleResearch |
| Version | 1.34.0 |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0), MultiAssayExperiment |
| Imports | AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors, stats, SummarizedExperiment, utils |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/waldronlab/curatedTCGAData/issues |
See More
| Suggests | BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | AMARETTO |
| Suggests Me | CNVRanger, glmSparseNet, imageFeatureTCGA, TCGAutils |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | curatedTCGAData_1.34.0.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/curatedTCGAData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/curatedTCGAData |
| Package Short Url | https://bioconductor.org/packages/curatedTCGAData/ |
| Package Downloads Report | Download Stats |