RTCGA
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see RTCGA.
The Cancer Genome Atlas Data Integration
Bioconductor version: Release (3.23)
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("RTCGA")):Marcin Kosinski. RTCGA: The Cancer Genome Atlas Data Integration. doi:10.18129/B9.bioc.RTCGA, R package version 1.41.0, https://bioconductor.org/packages/RTCGA.
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")
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 | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, DataImport, DataRepresentation, ImmunoOncology, Preprocessing, PrincipalComponent, RNASeq, Software, Survival, Visualization |
| Version | 1.41.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 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 |
See More
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RTCGA_1.41.0.tar.gz |
| Windows Binary (x86_64) | RTCGA_1.41.0.zip |
| macOS Binary (big-sur-x86_64) | RTCGA_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | RTCGA_1.41.0.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 |