curatedTCGAData
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see curatedTCGAData.
Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
Bioconductor version: 3.10
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]
Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>
citation("curatedTCGAData")):
Installation
To install this package, start R (version "3.6") 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 | 1.8.1 |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), MultiAssayExperiment |
| Imports | AnnotationHub, ExperimentHub, HDF5Array, S4Vectors, stats, SummarizedExperiment, utils |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/waldronlab/curatedTCGAData/issues |
See More
| Suggests | BiocStyle, knitr, readr, rmarkdown, TCGAutils, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | AMARETTO, BiocOncoTK |
| Suggests Me | CNVRanger, deco, glmSparseNet, TCGAutils |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | curatedTCGAData_1.8.1.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | |
| 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 |