https://github.com/cumbof/tcga2bed
The Cancer Genome Atlas Data Extraction and Conversion Tool
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 6 DOI reference(s) in README -
○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (4.5%) to scientific vocabulary
Keywords
Repository
The Cancer Genome Atlas Data Extraction and Conversion Tool
Basic Info
- Host: GitHub
- Owner: cumbof
- Language: Java
- Default Branch: master
- Homepage: http://bioinf.iasi.cnr.it/tcga2bed/
- Size: 14.9 MB
Statistics
- Stars: 1
- Watchers: 3
- Forks: 2
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
TCGA2BED
TCGA2BED is a Java software tool that allows searching and retrieving all public genomic and clinical 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), and transforming them in standard BED, GTF, CSV, and JSON format, which also allows comprehensively querying them with the GenoMetric Query Language (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/
Public data repository
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
Owner
- Name: Fabio Cumbo
- Login: cumbof
- Kind: user
- Location: Cleveland, OH, USA
- Company: Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic
- Website: https://cumbof.github.io/
- Twitter: cumbofabio
- Repositories: 14
- Profile: https://github.com/cumbof
Ph.D. in Computer Science and Automation Engineering, Postdoctoral Research Fellow @BlankenbergLab, GMI, LRI, Cleveland Clinic, USA
GitHub Events
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- Watch event: 1
Last Year
- Watch event: 1
Issues and Pull Requests
Last synced: about 1 year ago
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- Total issues: 1
- Total pull requests: 0
- Average time to close issues: 20 days
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- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
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- Average comments per issue: 0
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Top Authors
Issue Authors
- pradyumnasagar (1)