To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RTCGA")
In most cases, you don't need to download the package archive at all.
RTCGA
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The Cancer Genome Atlas Data Integration
Bioconductor version: Release (3.4)
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>
Citation (from within R,
enter citation("RTCGA")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RTCGA")
Documentation
| HTML | Integrating TCGA Data - RTCGA Workflow | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, DataRepresentation, Preprocessing, RNASeq, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (1.5 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | RTCGA_1.4.0.tar.gz |
| Windows Binary | RTCGA_1.4.0.zip |
| Mac OS X 10.9 (Mavericks) | RTCGA_1.4.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/RTCGA/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/RTCGA/ |
| Package Downloads Report | Download Stats |
Documentation »
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