curatedTCGAData

This is the development version of curatedTCGAData; for the stable release version, see curatedTCGAData.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6

Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

Bioconductor version: Development (3.24)

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] ORCID: 0000-0002-3242-0582 , 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 (from within R, enter citation("curatedTCGAData")):

Marcel Ramos. curatedTCGAData: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects. doi:10.18129/B9.bioc.curatedTCGAData, R package version 1.35.0, https://bioconductor.org/packages/curatedTCGAData.

Generated from the package metadata; it may differ from the package's own citation.

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("curatedTCGAData")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

No vignettes available
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CancerData, ExperimentData, ExperimentHub, Homo_sapiens_Data, ReproducibleResearch
Version	1.35.0
In Bioconductor since	BioC 3.6 (R-3.4) (9 years)
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

Suggests	BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat
Linking To
Enhances
Depends On Me
Imports Me	AMARETTO
Suggests Me	CNVRanger, glmSparseNet, imageFeatureTCGA, TCGAutils, TDbasedUFEadv
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	curatedTCGAData_1.35.0.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