datasetsTCGA: RTCGA.data - The Family of R Packages with Data from The...

In RTCGA: The Cancer Genome Atlas Data Integration

Description

Snapshots of the clinical, mutations, CNVs, rnaseq, RPPA, mRNA, miRNASeq and methylation datasets from the 2015-11-01 release date (check all dates of release with checkTCGA('Dates')) are included in the RTCGA.data family (factory) that contains 9 packages:

• RTCGA.rnaseq rnaseq

• RTCGA.clinical clinical

• RTCGA.mutations mutations

• RTCGA.CNV CNV

• RTCGA.RPPA RPPA

• RTCGA.mRNA mRNA

• RTCGA.miRNASeq miRNASeq

• RTCGA.methylation methylation

• RTCGA.PANCAN12 (not from TCGA)

Details

For more detailed information visit RTCGA.data website https://rtcga.github.io/RTCGA. One can install all data packages with installTCGA.

Issues

If you have any problems, issues or think that something is missing or is not clear please post an issue on https://github.com/RTCGA/RTCGA/issues.

Author(s)

Marcin Kosinski [aut, cre] [e-mail]
Przemyslaw Biecek [aut] [e-mail]
Witold Chodor [aut] [e-mail]

See Also

RTCGA website http://rtcga.github.io/RTCGA.

Other RTCGA: RTCGA-package, boxplotTCGA, checkTCGA, convertTCGA, downloadTCGA, expressionsTCGA, heatmapTCGA, infoTCGA, installTCGA, kmTCGA, mutationsTCGA, pcaTCGA, readTCGA, survivalTCGA, theme_RTCGA

Examples

# installation of packages containing snapshots
# of TCGA project's datasets

## Not run: 

## RTCGA GitHub development newest versions
library(RTCGA)
?installTCGA

## Bioconductor releases
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install(RTCGA.clinical)
BiocManager::install(RTCGA.mutations)
BiocManager::install(RTCGA.rnaseq)
BiocManager::install(RTCGA.CNV)
BiocManager::install(RTCGA.RPPA)
BiocManager::install(RTCGA.mRNA)
BiocManager::install(RTCGA.miRNASeq)
BiocManager::install(RTCGA.methylation)

# use cases and examples + more data info
browseVignettes('RTCGA')

## End(Not run)

RTCGA documentation built on Nov. 8, 2020, 5:11 p.m.