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https://bioinformaticsfmrp.github.io/TCGAbiolinks

TCGAbiolinks
https://bioinformaticsfmrp.github.io/TCGAbiolinks

bioc bioconductor gdc integrative-analysis r tcga tcga-data tcgabiolinks

Last synced: 2 months ago
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TCGAbiolinks

Host: GitHub
URL: https://bioinformaticsfmrp.github.io/TCGAbiolinks
Owner: BioinformaticsFMRP
Created: 2015-03-02T14:56:03.000Z (almost 10 years ago)
Default Branch: master
Last Pushed: 2024-08-08T01:46:08.000Z (5 months ago)
Last Synced: 2024-09-16T14:19:25.751Z (3 months ago)
Topics: bioc, bioconductor, gdc, integrative-analysis, r, tcga, tcga-data, tcgabiolinks
Language: R
Homepage: http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
Size: 349 MB
Stars: 289
Watchers: 25
Forks: 110
Open Issues: 256
Metadata Files:
- Readme: README.md

Awesome Lists containing this project

awesome-TCGA - TCGABiolinks - A R/Bioconductor package to search, download and prepare relevant data for analysis in R. Very powerful and well documented. (Downloading the data / Others)

README

        [![Build Status](https://travis-ci.org/BioinformaticsFMRP/TCGAbiolinks.svg?branch=master)](https://travis-ci.org/BioinformaticsFMRP/TCGAbiolinks)

[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/BioinformaticsFMRP/TCGAbiolinks?branch=master&svg=true)](https://ci.appveyor.com/project/BioinformaticsFMRP/TCGAbiolinks)

[![codecov.io](https://codecov.io/github/BioinformaticsFMRP/TCGAbiolinks/coverage.svg?branch=master)](https://codecov.io/github/BioinformaticsFMRP/TCGAbiolinks?branch=master)

[![bioc](http://www.bioconductor.org/shields/years-in-bioc/TCGAbiolinks.svg)](http://bioconductor.org/packages/TCGAbiolinks/)

[![bioc](http://bioconductor.org/shields/availability/devel/TCGAbiolinks.svg)](http://bioconductor.org/packages/TCGAbiolinks/)

------------------------------------------------------------------------

# TCGAbiolinks - An R/Bioconductor package for integrative analysis with TCGA data

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.

### Installation from GitHub ###

```R

if (!requireNamespace("BiocManager", quietly = TRUE))

    install.packages("BiocManager")

BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")

BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

```

### Installation from Bioconductor ###

```R

if (!requireNamespace("BiocManager", quietly = TRUE))

    install.packages("BiocManager")

BiocManager::install("TCGAbiolinks")

```

------------------------------------------------------------------------

### Docker image ###

TCGAbiolinks is available as Docker image (self-contained environments that contain everything needed to run the software), 

which can be easily run on Mac OS, Windows and Linux systems. 

This [PDF](https://drive.google.com/open?id=0B0-8N2fjttG-QXp5LVlPQnVQejg) show how to install and execute the image.

The image can be obtained from Docker Hub: https://hub.docker.com/r/tiagochst/tcgabiolinksgui/

For more information please check: https://docs.docker.com/ and https://www.bioconductor.org/help/docker/

### Manual ###

http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html

------------------------------------------------------------------------

## Citation

Please cite both TCGAbiolinks package: 

* Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, Sabedot T, Malta TM, Pagnotta SM, Castiglioni I, Ceccarelli M, Bontempi G and Noushmehr H. "TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data." Nucleic acids research (2015): gkv1507.

* Mounir, Mohamed, Lucchetta, Marta, Silva, C T, Olsen, Catharina, Bontempi, Gianluca, Chen, Xi, Noushmehr, Houtan, Colaprico, Antonio, Papaleo, Elena (2019). “New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx.” PLoS computational biology, 15(3), e1006701.

* Silva TC, Colaprico A, Olsen C et al.TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; peer review: 1 approved, 2 approved with reservations]. F1000Research 2016, 5:1542

(https://doi.org/10.12688/f1000research.8923.2)

[![doi](https://img.shields.io/badge/doi-10.1093/nar/gkv1507-green.svg?style=flat)](http://dx.doi.org/10.1093/nar/gkv1507) [![citation](https://img.shields.io/badge/cited%20by-1151-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=15937881581405647591) [![Altmetric](https://img.shields.io/badge/Altmetric-44-green.svg?style=flat)](https://www.altmetric.com/details/4919535)

Also, if you have used ELMER analysis please cite:

* Yao, L., Shen, H., Laird, P. W., Farnham, P. J., & Berman, B. P. "Inferring regulatory element landscapes and transcription factor networks from cancer methylomes." Genome Biol 16 (2015): 105.

* Yao, Lijing, Benjamin P. Berman, and Peggy J. Farnham. "Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes." Critical reviews in biochemistry and molecular biology 50.6 (2015): 550-573.

* Tiago C Silva, Simon G Coetzee, Nicole Gull, Lijing Yao, Dennis J Hazelett, Houtan Noushmehr, De-Chen Lin, Benjamin P Berman, ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles, Bioinformatics, Volume 35, Issue 11, 1 June 2019, Pages 1974–1977, https://doi.org/10.1093/bioinformatics/bty902