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 aarch64-apple-darwin20
## arch aarch64
## os darwin20
## system aarch64, darwin20
## status
## major 4
## minor 2.1
## year 2022
## month 06
## day 23
## svn rev 82513
## language R
## version.string R version 4.2.1 (2022-06-23)
## nickname Funny-Looking Kid
packageVersion("TCGAbiolinks")
## [1] '2.25.3'