{"id":19857022,"url":"https://github.com/griffithlab/regtools","last_synced_at":"2025-10-13T22:40:22.114Z","repository":{"id":32267142,"uuid":"35841695","full_name":"griffithlab/regtools","owner":"griffithlab","description":"Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.","archived":false,"fork":false,"pushed_at":"2024-08-21T03:30:14.000Z","size":6362,"stargazers_count":130,"open_issues_count":45,"forks_count":28,"subscribers_count":12,"default_branch":"master","last_synced_at":"2025-06-10T02:40:45.629Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://regtools.readthedocs.org","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/griffithlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-05-18T20:46:35.000Z","updated_at":"2025-05-28T18:35:48.000Z","dependencies_parsed_at":"2024-08-21T04:55:24.777Z","dependency_job_id":null,"html_url":"https://github.com/griffithlab/regtools","commit_stats":null,"previous_names":[],"tags_count":10,"template":false,"template_full_name":null,"purl":"pkg:github/griffithlab/regtools","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fregtools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fregtools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fregtools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fregtools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/griffithlab","download_url":"https://codeload.github.com/griffithlab/regtools/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fregtools/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279017145,"owners_count":26085984,"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","status":"online","status_checked_at":"2025-10-13T02:00:06.723Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2024-11-12T14:17:14.947Z","updated_at":"2025-10-13T22:40:22.098Z","avatar_url":"https://github.com/griffithlab.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"![Build Status](https://github.com/griffithlab/regtools/actions/workflows/cmake.yml/badge.svg?branch=master)\n[![Documentation Status](https://readthedocs.org/projects/regtools/badge/?version=latest)](https://readthedocs.org/projects/regtools/?badge=latest)\n[![Coverage Status](https://coveralls.io/repos/griffithlab/regtools/badge.svg?branch=master\u0026service=github)](https://coveralls.io/github/griffithlab/regtools?branch=master)\n\n# RegTools\n\nTools that integrate DNA-seq and RNA-seq data to help interpret mutations\nin a regulatory and splicing context.\n\n## Features\n\n- Identify evidence for aberrant splicing in RNA reads near a list of variants.\n- Extract exon-exon junctions from a RNAseq BAM file.\n- Annotate exon-exon junctions with information from a known transcriptome.\n- Annotate variants with splice-region(the definition of this region is configurable) annotations.\n\n## Hardware requirements\nRegTools  requires only a standard computer with enough RAM to support the in-memory operations.\n\n## Software requirements\nOS Requirements\nThis package is supported for macOS and Linux. The package has been tested on the following systems:\n\nmacOS: macOS 10.12 (Sierra), macOS 10.13 (High Sierra), macOS 10.14 (Mojave), macOS 10.15 (Catalina), macOS 11 (Big Sur), macOS 12 (Monterey)\n\nLinux: Ubuntu 16.04, Ubuntu 18.04, Ubuntu 20.04\n\n## Installation\n\nClone and install regtools by running the following:\n```\n    git clone https://github.com/griffithlab/regtools\n    cd regtools/\n    mkdir build\n    cd build/\n    cmake ..\n    make\n```\n\nInstallation should take 1-5 minutes.\n\nFor convienience we also maintain a docker image available at [https://hub.docker.com/r/griffithlab/regtools/](https://hub.docker.com/r/griffithlab/regtools/)\n\n## Usage:\n\n```\n    regtools --help\n```\n\nIf one wishes to test their installation, we include test data under `test_data`. \n\nHere's an example command using that data along with the example output. This should run in under a minute.\n\n```sh\nregtools cis-splice-effects identify -s RF -e 10 -i 10 test_data/HCC1395_chr22.vcf.gz test_data/HCC1395_tumor.bam test_data/chr22_with_ERCC92.fa test_data/chr22_with_ERCC92.gtf\n\nVariant 22\t42129188\t42129189\t-1\nVariant region is 22:42128784-42130813\n\nchrom\tstart\tend\tname\tscore\tstrand\tsplice_site\tacceptors_skipped\texons_skipped\tdonors_skipped\tanchor\tknown_donor\tknown_acceptor\tknown_junction\tgene_names\tgene_ids\ttranscripts\tvariant_info\nposition = 22:42125408-42125409\nposition = 22:42130565-42130566\n22\t42125407\t42130567\tJUNC00000001\t4\t+\tGT-AG\t0\t0\t0\tD\t1\t0\t0\tNDUFA6-AS1\tENSG00000237037\tENST00000439129\t22:42129188-42129189\nposition = 22:42128881-42128882\nposition = 22:42129670-42129671\n22\t42128880\t42129672\tJUNC00000002\t3\t+\tGT-AG\t0\t0\t0\tN\t0\t0\t0\tNA\tNA\tNA\t22:42129188-42129189\nposition = 22:42128944-42128945\nposition = 22:42129031-42129032\n22\t42128943\t42129033\tJUNC00000003\t4\t-\tGT-GG\t1\t0\t0\tD\t1\t0\t0\tCYP2D6\tENSG00000100197\tENST00000360608,ENST00000389970,ENST00000488442\t22:42129188-42129189\nposition = 22:42129783-42129784\nposition = 22:42143453-42143454\n22\t42129782\t42143455\tJUNC00000004\t2\t+\tGC-AG\t9\t8\t9\tN\t0\t0\t0\tNA\tNA\tNA\t22:42129188-42129189\nposition = 22:42130224-42130225\nposition = 22:42130565-42130566\n22\t42130223\t42130567\tJUNC00000005\t2\t+\tGT-AG\t0\t0\t0\tN\t0\t0\t0\tNA\tNA\tNA\t22:42129188-42129189\n```\n\n## Contribute\n\n- Issue Tracker: github.com/griffithlab/regtools/issues\n- Source Code: github.com/griffithlab/regtools\n\n## Support\n\nIf you have issues using the project, please let us know.\nWe have a mailing list located at: regtools@googlegroups.com and the\nforum is here - https://groups.google.com/forum/#!forum/regtools.\nGithub issues are another option to contact the project about\npotential bugs.\n\n## Documentation\n\nThe documentation for the project is hosted on\n[Read the Docs.](https://regtools.readthedocs.org/en/latest/)\n\nIf you would like to build the documentation locally, please install\n[mkdocs](http://www.mkdocs.org/), `pip install mkdocs --user` should\nwork on most machines. Then run `mkdocs serve` from within the `regtools`\nbase directory.\n\n\n## Acknowledgements\n\nRegtools uses several open-source libraries. We would like to thank the\ndevelopers of htslib and bedtools. We would also like to thank Travis Abbott for\nuseful comments and code.\n\n## License\n\nThe project is licensed under the [MIT license](https://opensource.org/licenses/MIT).\n\n## Stable release with DOI\n\n[![DOI](https://zenodo.org/badge/35841695.svg)](https://zenodo.org/badge/latestdoi/35841695)\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fregtools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgriffithlab%2Fregtools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fregtools/lists"}