{"id":20425006,"url":"https://github.com/databio/pepatac","last_synced_at":"2025-10-13T01:20:48.860Z","repository":{"id":43209183,"uuid":"58678230","full_name":"databio/pepatac","owner":"databio","description":"A modular, containerized pipeline for ATAC-seq data processing","archived":false,"fork":false,"pushed_at":"2025-09-23T17:08:02.000Z","size":22924,"stargazers_count":59,"open_issues_count":55,"forks_count":16,"subscribers_count":21,"default_branch":"master","last_synced_at":"2025-09-23T19:09:47.478Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://pepatac.databio.org","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-2-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/databio.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2016-05-12T21:29:13.000Z","updated_at":"2025-09-23T17:07:14.000Z","dependencies_parsed_at":"2023-01-21T21:49:49.115Z","dependency_job_id":"63b574fd-f63f-438d-9818-a70ec44c4cc5","html_url":"https://github.com/databio/pepatac","commit_stats":{"total_commits":1337,"total_committers":14,"mean_commits":95.5,"dds":"0.40762902019446523","last_synced_commit":"9ea1043cb2eba3194a30c0f759a7cc3316c8b139"},"previous_names":[],"tags_count":49,"template":false,"template_full_name":null,"purl":"pkg:github/databio/pepatac","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fpepatac","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fpepatac/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fpepatac/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fpepatac/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/databio","download_url":"https://codeload.github.com/databio/pepatac/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fpepatac/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279013886,"owners_count":26085325,"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":"2025-10-12T02:00:06.719Z","response_time":53,"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":"2024-11-15T07:11:56.356Z","updated_at":"2025-10-13T01:20:48.822Z","avatar_url":"https://github.com/databio.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg src=\"docs/img/pepatac_logo_white.svg\" alt=\"pepatac logo\" height=\"70\" align=\"left\"/\u003e\n\n\u003cbr\u003e\u003c/br\u003e\n\n---\n\n[![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)\n\nPEPATAC is a pipeline for ATAC-seq data. For more information see: http://pepatac.databio.org/\n\n## Docs\n\nDevelop docs with:\n\n```\nmkdocs serve -f mkdocs.yml\n```\n\nBuild and deploy with:\n\n```\nmkdocs build -f mkdocs.yml -d $CODEBASE/code.databio.org/pepatac/\n```\n\n## Contributing\n\nPull requests welcome. Active development should occur in a development or feature branch.\n\n## Contributors\n\n* Jason Smith, jasonsmith@virginia.edu\n* Nathan Sheffield, nathan@code.databio.org\n* Jin Xu, jinxu9@stanford.edu\n* Ryan Corces, rcorces@stanford.edu\n* Vince Reuter, vreuter@protonmail.com\n* Donald Campbell, https://github.com/donaldcampbelljr\n* Others... (add your name)\n\n## Citing\n\nIf you find PEPATAC useful in your research, please cite: \n\nJason P. Smith, M. Ryan Corces, Jin Xu, Vincent P. Reuter, Howard Y. Chang, and Nathan C. Sheffield. \u003cb\u003ePEPATAC: An optimized ATAC-seq pipeline with serial alignments.\u003c/b\u003e \u003ci\u003ebioRxiv\u003c/i\u003e (2021). \u003ca href=\"https://doi.org/10.1101/2020.10.21.347054\"\u003eDOI: 10.1101/2020.10.21.347054\u003c/a\u003e\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fpepatac","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabio%2Fpepatac","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fpepatac/lists"}