https://github.com/cumbof/tcga2bed
The Cancer Genome Atlas Data Extraction and Conversion Tool
https://github.com/cumbof/tcga2bed
bed clinical converter genomic gmql repository tcga
Last synced: 10 months ago
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The Cancer Genome Atlas Data Extraction and Conversion Tool
- Host: GitHub
- URL: https://github.com/cumbof/tcga2bed
- Owner: cumbof
- Archived: true
- Created: 2017-03-12T15:37:50.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2020-04-02T11:44:40.000Z (about 6 years ago)
- Last Synced: 2025-03-21T16:48:18.097Z (about 1 year ago)
- Topics: bed, clinical, converter, genomic, gmql, repository, tcga
- Language: Java
- Homepage: http://bioinf.iasi.cnr.it/tcga2bed/
- Size: 14.9 MB
- Stars: 1
- Watchers: 3
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# TCGA2BED
TCGA2BED is a Java software tool that allows searching and retrieving all public [genomic](https://wiki.nci.nih.gov/display/TCGA/TCGA+Encyclopedia) and [clinical](https://wiki.nci.nih.gov/display/TCGA/Clinical+data) data of DNA-Seq, RNA-Seq (V1 and V2), DNA-Methylation, miRNA-Seq and CNV from one of the largest public repositories of cancer genomic data, [The Cancer Genome Atlas (TCGA)](http://cancergenome.nih.gov/), and transforming them in standard BED, GTF, CSV, and JSON format, which also allows comprehensively querying them with the [GenoMetric Query Language (GMQL)](http://www.bioinformatics.deib.polimi.it/GMQL/). A user-friendly interface is available to search, download, and convert all the public TCGA cancer related data sets.
### Software web-page
[http://bioinf.iasi.cnr.it/tcga2bed/](http://bioinf.iasi.cnr.it/tcga2bed/)
### Public data repository
[ftp://bioinf.iasi.cnr.it/](ftp://bioinf.iasi.cnr.it/)
### Credits
Please credit TCGA2BED in your manuscript by citing:
> Fabio Cumbo, Giulia Fiscon, Stefano Ceri, Marco Masseroli, and Emanuel Weitschek. "TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas." BMC Bioinformatics (2017) 18 1:6. [https://dx.doi.org/10.1186/s12859-016-1419-5](https://dx.doi.org/10.1186/s12859-016-1419-5)