TCGAbiolinks - Cancer Science

What is TCGAbiolinks?

TCGAbiolinks is an R/Bioconductor package designed to facilitate the retrieval, analysis, and visualization of cancer genomics data from The Cancer Genome Atlas (TCGA). It provides a comprehensive toolset for bioinformatics researchers to work with large-scale cancer datasets, making it easier to download, preprocess, and analyze genomic data.

Why is TCGAbiolinks Important for Cancer Research?

The vast amount of data generated by TCGA includes genomic, epigenomic, transcriptomic, and proteomic data. TCGAbiolinks simplifies access to this data, offering functionalities for data integration and analysis that are crucial for understanding cancer biology. By using TCGAbiolinks, researchers can perform complex analyses such as differential expression, enrichment analysis, and survival analysis, which can lead to the discovery of novel biomarkers and therapeutic targets.

How to Install TCGAbiolinks?

Installing TCGAbiolinks is straightforward. It can be installed from Bioconductor using the following commands in R:

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TCGAbiolinks")

Once installed, you can load the package using:

library(TCGAbiolinks)

What Types of Data Can Be Accessed with TCGAbiolinks?

TCGAbiolinks provides access to a variety of data types from TCGA, including:

Genomic Data (e.g., somatic mutations, copy number variations)
Transcriptomic Data (e.g., mRNA expression, miRNA expression)
Epigenomic Data (e.g., DNA methylation)
Clinical Data (e.g., patient demographics, clinical outcomes)

How to Retrieve Data Using TCGAbiolinks?

Data can be retrieved using the GDCquery function. Here is an example of how to query and download RNA-seq data for breast cancer:

query

Relevant Publications

ATG9B Is a Poor Prognostic Marker Associated With Immune Evasion in Colon Adenocarcinoma.

Issue Release: 2023

Stage Analysis of Breast Cancer Metabolomics: A System Biology Approach.

Issue Release: 2023

Loss of STARD13 contributes to aggressive phenotype transformation and poor prognosis in papillary thyroid carcinoma.

Issue Release: 2023

Identification of a chemoresistance-related prognostic gene signature by comprehensive analysis and experimental validation in pancreatic cancer.

Issue Release: 2023

Analysis of transcript-wide profile regulated by microsatellite instability of colorectal cancer.

Issue Release: 2022

Analysis of endometrial carcinoma TCGA reveals differences in DNA methylation in tumors from Black and White women.

Issue Release: 2022

Rediscover: an R package to identify mutually exclusive mutations.

Issue Release: 2022

Pan-cancer gene expression analysis: Identification of deregulated autophagy genes and drugs to target them.

Issue Release: 2022

MMRFBiolinks: an R-package for integrating and analyzing MMRF-CoMMpass data.

Issue Release: 2021

A stacking ensemble deep learning approach to cancer type classification based on TCGA data.

Issue Release: 2021

Molecular description of ANGPT2 associated colorectal carcinoma.

Issue Release: 2020

Landscape of transcription and expression regulated by DNA methylation related to age of donor and cell passage in adipose-derived mesenchymal stem cells.

Issue Release: 2020

Bioinformatics Analysis of Differentially Expressed Genes and miRNAs in Low-Grade Gliomas.

Issue Release: 2020

New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx.

Issue Release: 2019

Long Noncoding RNA ASB16-AS1 Promotes Proliferation, Migration, and Invasion in Glioma Cells.

Issue Release: 2019

DCARS: differential correlation across ranked samples.

Issue Release: 2019

Analysis of the Cancer Genome Atlas Data Reveals Novel Putative ncRNAs Targets in Hepatocellular Carcinoma.

Issue Release: 2018

Identification of a 5‑microRNA signature and hub miRNA‑mRNA interactions associated with pancreatic cancer.

Issue Release: 2018

Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex.

Issue Release: 2017

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.

Issue Release: 2015

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