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This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see RTCGA.

The Cancer Genome Atlas Data Integration

Bioconductor version: 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>, Przemyslaw Biecek <przemyslaw.biecek at>

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

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


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


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
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
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
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Package Source RTCGA_1.4.0.tar.gz
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