RTCGA

DOI: 10.18129/B9.bioc.RTCGA    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RTCGA.

The Cancer Genome Atlas Data Integration

Bioconductor version: 3.12

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 <m.p.kosinski at gmail.com>, Przemyslaw Biecek <przemyslaw.biecek at gmail.com>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	DataImport, DataRepresentation, ImmunoOncology, Preprocessing, RNASeq, Software
Version	1.20.0
In Bioconductor since	BioC 3.2 (R-3.2) (5.5 years)
License	GPL-2
Depends	R (>= 3.3.0)
Imports	XML, assertthat, stringi, rvest, data.table, xml2, dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr, scales
LinkingTo
Suggests	devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, RTCGA.PANCAN12, magrittr, tidyr
SystemRequirements
Enhances
URL	https://rtcga.github.io/RTCGA
BugReports	https://github.com/RTCGA/RTCGA/issues
Depends On Me	RTCGA.clinical, RTCGA.CNV, RTCGA.methylation, RTCGA.miRNASeq, RTCGA.mRNA, RTCGA.mutations, RTCGA.PANCAN12, RTCGA.rnaseq, RTCGA.RPPA
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	RTCGA_1.20.0.tar.gz
Windows Binary	RTCGA_1.20.0.zip
macOS 10.13 (High Sierra)	RTCGA_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RTCGA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RTCGA
Package Short Url	https://bioconductor.org/packages/RTCGA/
Package Downloads Report	Download Stats