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RTCGA

The Cancer Genome Atlas Data Integration

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews DNAMethylation, DataImport, DataRepresentation, ImmunoOncology, Preprocessing, PrincipalComponent, RNASeq, Software, Survival, Visualization
Version 1.30.0
In Bioconductor since BioC 3.2 (R-3.2) (8 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
Linking To
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
System Requirements
Enhances
URL https://rtcga.github.io/RTCGA
Bug Reports https://github.com/RTCGA/RTCGA/issues
See More
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  

Package Archives

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

Source Package RTCGA_1.30.0.tar.gz
Windows Binary RTCGA_1.30.0.zip (64-bit only)
macOS Binary (x86_64) RTCGA_1.30.0.tgz
macOS Binary (arm64) RTCGA_1.30.0.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