RTCGA: The Cancer Genome Atlas Data Integration

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@gmail.com>, Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Date of publication
None
Maintainer
Marcin Kosinski <m.p.kosinski@gmail.com>
License
GPL-2
Version
1.4.0
URLs

View on Bioconductor

Man pages

boxplotTCGA
Create Boxplots for TCGA Datasets
checkTCGA
Information about datasets from TCGA project
convertTCGA
Convert data from RTCGA family to Bioconductor classes
datasetsTCGA
RTCGA.data - The Family of R Packages with Data from The...
downloadTCGA
Download TCGA data
expressionsTCGA
Gather Expressions for TCGA Datasets
heatmapTCGA
Create Heatmaps for TCGA Datasets
infoTCGA
Information about cohorts from TCGA project
installTCGA
Install packages from RTCGA family
kmTCGA
Plot Kaplan-Meier Estimates of Survival Curves for Survival...
mutationsTCGA
Gather Mutations for TCGA Datasets
pcaTCGA
Plot Two Main Components of Principal Component Analysis
readTCGA
Read TCGA data to the tidy format
RTCGA-package
The Caner Genome Atlas data integration
survivalTCGA
Extract Survival Information From RTCGA.clinical Datasets
theme_RTCGA
RTCGA Theme For ggplot2

Files in this package

RTCGA/DESCRIPTION
RTCGA/NAMESPACE
RTCGA/NEWS
RTCGA/R
RTCGA/R/RTCGA-package.R
RTCGA/R/boxplotTCGA.R
RTCGA/R/checkTCGA.R
RTCGA/R/convertTCGA.R
RTCGA/R/datasetsTCGA.R
RTCGA/R/downloadTCGA.R
RTCGA/R/expressionTCGA.R
RTCGA/R/ggbiplot.R
RTCGA/R/heatmapTCGA.R
RTCGA/R/infoTCGA.R
RTCGA/R/installTCGA.R
RTCGA/R/kmTCGA.R
RTCGA/R/mutationsTCGA.R
RTCGA/R/pcaTCGA.R
RTCGA/R/readTCGA.R
RTCGA/R/survivalTCGA.R
RTCGA/R/theme_RTCGA.R
RTCGA/R/zzz.R
RTCGA/README.md
RTCGA/build
RTCGA/build/vignette.rds
RTCGA/inst
RTCGA/inst/doc
RTCGA/inst/doc/RTCGA_Workflow.Rmd
RTCGA/inst/doc/RTCGA_Workflow.html
RTCGA/man
RTCGA/man/RTCGA-package.Rd
RTCGA/man/boxplotTCGA.Rd
RTCGA/man/checkTCGA.Rd
RTCGA/man/convertTCGA.Rd
RTCGA/man/datasetsTCGA.Rd
RTCGA/man/downloadTCGA.Rd
RTCGA/man/expressionsTCGA.Rd
RTCGA/man/heatmapTCGA.Rd
RTCGA/man/infoTCGA.Rd
RTCGA/man/installTCGA.Rd
RTCGA/man/kmTCGA.Rd
RTCGA/man/mutationsTCGA.Rd
RTCGA/man/pcaTCGA.Rd
RTCGA/man/readTCGA.Rd
RTCGA/man/survivalTCGA.Rd
RTCGA/man/theme_RTCGA.Rd
RTCGA/tests
RTCGA/tests/testthat
RTCGA/tests/testthat.R
RTCGA/tests/testthat/test_check.R
RTCGA/tests/testthat/test_convert.R
RTCGA/tests/testthat/test_download.R
RTCGA/tests/testthat/test_info.R
RTCGA/tests/testthat/test_read.R
RTCGA/vignettes
RTCGA/vignettes/RTCGA_Workflow.Rmd