{"id":21845367,"url":"https://github.com/cumbof/tcga2bed","last_synced_at":"2025-07-20T19:31:54.530Z","repository":{"id":68348082,"uuid":"84736773","full_name":"cumbof/TCGA2BED","owner":"cumbof","description":"The Cancer Genome Atlas Data Extraction and Conversion Tool","archived":true,"fork":false,"pushed_at":"2020-04-02T11:44:40.000Z","size":15665,"stargazers_count":1,"open_issues_count":0,"forks_count":2,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-21T16:48:18.097Z","etag":null,"topics":["bed","clinical","converter","genomic","gmql","repository","tcga"],"latest_commit_sha":null,"homepage":"http://bioinf.iasi.cnr.it/tcga2bed/","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cumbof.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-03-12T15:37:50.000Z","updated_at":"2024-11-26T09:02:21.000Z","dependencies_parsed_at":null,"dependency_job_id":"77c78a8a-0e51-4e2c-87d4-3b04647d10d3","html_url":"https://github.com/cumbof/TCGA2BED","commit_stats":null,"previous_names":["fabio-cumbo/tcga2bed"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/cumbof/TCGA2BED","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cumbof%2FTCGA2BED","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cumbof%2FTCGA2BED/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cumbof%2FTCGA2BED/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cumbof%2FTCGA2BED/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cumbof","download_url":"https://codeload.github.com/cumbof/TCGA2BED/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cumbof%2FTCGA2BED/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266187041,"owners_count":23889903,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bed","clinical","converter","genomic","gmql","repository","tcga"],"created_at":"2024-11-27T23:09:38.464Z","updated_at":"2025-07-20T19:31:51.167Z","avatar_url":"https://github.com/cumbof.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"# TCGA2BED\nTCGA2BED 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.\n\n### Software web-page\n[http://bioinf.iasi.cnr.it/tcga2bed/](http://bioinf.iasi.cnr.it/tcga2bed/)\n\n### Public data repository\n[ftp://bioinf.iasi.cnr.it/](ftp://bioinf.iasi.cnr.it/)\n\n### Credits\n\nPlease credit TCGA2BED in your manuscript by citing:\n\n\u003e 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)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcumbof%2Ftcga2bed","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcumbof%2Ftcga2bed","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcumbof%2Ftcga2bed/lists"}