RTCGA

The Cancer Genome Atlas Data Integration

Bioconductor version: Release (3.19)

The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients' treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.

Author: Marcin Kosinski [aut, cre], Przemyslaw Biecek [ctb], Witold Chodor [ctb]

Maintainer: Marcin Kosinski <m.p.kosinski at gmail.com>

Citation (from within R, enter citation("RTCGA")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RTCGA")

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("RTCGA")

Integrating TCGA Data - RTCGA Workflow	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, DataImport, DataRepresentation, ImmunoOncology, Preprocessing, PrincipalComponent, RNASeq, Software, Survival, Visualization
Version	1.34.0
In Bioconductor since	BioC 3.2 (R-3.2) (9 years)
License	GPL-2
Depends	R (>= 3.3.0)
Imports	XML, RCurl, assertthat, stringi, rvest, data.table, xml2, dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr, scales, rmarkdown, htmltools
System Requirements
URL	https://rtcga.github.io/RTCGA
Bug Reports	https://github.com/RTCGA/RTCGA/issues

Suggests	devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, magrittr, tidyr
Linking To
Enhances
Depends On Me	RTCGA.clinical, RTCGA.CNV, RTCGA.methylation, RTCGA.miRNASeq, RTCGA.mRNA, RTCGA.mutations, RTCGA.PANCAN12, RTCGA.rnaseq, RTCGA.RPPA
Imports Me	TDbasedUFEadv
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	RTCGA_1.34.0.tar.gz
Windows Binary (x86_64)	RTCGA_1.34.0.zip
macOS Binary (x86_64)	RTCGA_1.34.0.tgz
macOS Binary (arm64)	RTCGA_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RTCGA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RTCGA
Bioc Package Browser	https://code.bioconductor.org/browse/RTCGA/
Package Short Url	https://bioconductor.org/packages/RTCGA/
Package Downloads Report	Download Stats