TCGAbiolinks is able to access The National Cancer Institute (NCI)
Genomic Data Commons (GDC) thorough its
GDC
Application Programming Interface (API) to search, download and
prepare relevant data for analysis in R.
If you use TCGAbiolinks, please cite:
Gao, Galen F., et al. “Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data.” Cell systems 9.1 (2019): 24-34. (https://doi.org/10.1016/j.cels.2019.06.006)
TCGA Workflow Analyze cancer genomics and epigenomics data using Bioconductor packages: http://bioconductor.org/packages/TCGAWorkflow/
You can install the stable version from Bioconductor. If you are having issues with the stable version, try using the development version.
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
::install("TCGAbiolinks") BiocManager
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")
BiocManager::install("BioinformaticsFMRP/TCGAbiolinks") BiocManager
The examples in this tutorial use the following libraries:
library(TCGAbiolinks)
library(dplyr)
library(DT)
version
## _
## platform x86_64-apple-darwin17.0
## arch x86_64
## os darwin17.0
## system x86_64, darwin17.0
## status Patched
## major 4
## minor 2.1
## year 2022
## month 07
## day 09
## svn rev 82577
## language R
## version.string R version 4.2.1 Patched (2022-07-09 r82577)
## nickname Funny-Looking Kid
packageVersion("TCGAbiolinks")
## [1] '2.26.0'