{"id":39806036,"url":"https://github.com/talusbio/nf-encyclopedia","last_synced_at":"2026-01-18T12:38:27.337Z","repository":{"id":45756371,"uuid":"417588378","full_name":"TalusBio/nf-encyclopedia","owner":"TalusBio","description":"A NextFlow pipeline for chromatogram library DIA proteomics workflows","archived":false,"fork":false,"pushed_at":"2023-12-04T23:16:24.000Z","size":19322,"stargazers_count":7,"open_issues_count":5,"forks_count":4,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-12-09T09:02:18.375Z","etag":null,"topics":["bioinformatics","data-independent-acquisition","nextflow","pipeline","proteomics","workflow"],"latest_commit_sha":null,"homepage":"","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/TalusBio.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.md","codeowners":null,"security":null,"support":null}},"created_at":"2021-10-15T17:50:02.000Z","updated_at":"2025-05-03T12:13:19.000Z","dependencies_parsed_at":"2023-01-29T00:30:25.378Z","dependency_job_id":null,"html_url":"https://github.com/TalusBio/nf-encyclopedia","commit_stats":null,"previous_names":[],"tags_count":42,"template":false,"template_full_name":null,"purl":"pkg:github/TalusBio/nf-encyclopedia","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TalusBio%2Fnf-encyclopedia","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TalusBio%2Fnf-encyclopedia/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TalusBio%2Fnf-encyclopedia/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TalusBio%2Fnf-encyclopedia/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/TalusBio","download_url":"https://codeload.github.com/TalusBio/nf-encyclopedia/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TalusBio%2Fnf-encyclopedia/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28536002,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-18T10:13:46.436Z","status":"ssl_error","status_checked_at":"2026-01-18T10:13:11.045Z","response_time":98,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["bioinformatics","data-independent-acquisition","nextflow","pipeline","proteomics","workflow"],"created_at":"2026-01-18T12:38:26.702Z","updated_at":"2026-01-18T12:38:27.329Z","avatar_url":"https://github.com/TalusBio.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# nf-encyclopedia\n\nnf-encyclopedia is a NextFlow pipeline specifically designed to analyze DIA proteomics experiment that leverage chromatogram libraries; however it is perfectly suited to analyze DIA proteomics experiments without chromatogram libraries as well. \nThe nf-encyclopedia connects three open-source tools---MSconvert, EncyclopeDIA, and MSstats---to go from mass spectra to quantified peptides and proteins. \n\nSee the [nf-encyclopedia documentation](https://TalusBio.github.io/nf-encyclopedia)\n\n## Development\n### Running Tests\nWe use the [pytest](https://docs.pytest.org/en/7.0.x/contents.html) Python package to run our tests. It can be installed using conda:\n\n``` sh\nconda env create --name nf_encyclopedia --file=environment.yml\nconda activate nf_encyclopedia\nconda install pytest\n```\n\nOnce installed, tests can be run from the root directory of the workflow.\nRun them with:\n\n``` sh\ndocker pull ghcr.io/talusbio/nf-encyclopedia:latest\npytest\n```\n\n## References\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) initiative, and reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).\n\n\u003e The nf-core framework for community-curated bioinformatics pipelines.\n\u003e\n\u003e Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso \u0026 Sven Nahnsen.\n\u003e\n\u003e Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n\n## Credits\n\nThis pipeline was originally written by @ricomnl and @wfondrie at Talus Bio. \nAdditionally, @cia23 has spent numerous hours reviewing @wfondrie's messy PRs and performing validation experiments. \n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftalusbio%2Fnf-encyclopedia","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftalusbio%2Fnf-encyclopedia","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftalusbio%2Fnf-encyclopedia/lists"}