curatedTCGAData
Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
Bioconductor version: Release (3.20)
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 "4.4") 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 | 1.28.0 |
License | Artistic-2.0 |
Depends | 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, TCGAutils, dce, glmSparseNet |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | curatedTCGAData_1.28.0.tar.gz |
Windows Binary (x86_64) | |
macOS Binary (x86_64) | |
macOS Binary (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 |