{"id":16637769,"url":"https://github.com/olegs/bioinformatics","last_synced_at":"2025-06-26T09:03:46.332Z","repository":{"id":139230771,"uuid":"83233874","full_name":"olegs/bioinformatics","owner":"olegs","description":"Reviews on NGS data analysis methods","archived":false,"fork":false,"pushed_at":"2019-05-03T18:18:18.000Z","size":30367,"stargazers_count":6,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-01-18T12:12:56.727Z","etag":null,"topics":["atac-seq","chip-seq","differential-chip-seq"],"latest_commit_sha":null,"homepage":"","language":"TeX","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/olegs.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":"2017-02-26T19:17:39.000Z","updated_at":"2024-03-13T05:32:29.000Z","dependencies_parsed_at":null,"dependency_job_id":"6c41af77-4dda-4c89-9f87-d2dee9f9f4fb","html_url":"https://github.com/olegs/bioinformatics","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/olegs%2Fbioinformatics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/olegs%2Fbioinformatics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/olegs%2Fbioinformatics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/olegs%2Fbioinformatics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/olegs","download_url":"https://codeload.github.com/olegs/bioinformatics/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243141727,"owners_count":20242925,"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":["atac-seq","chip-seq","differential-chip-seq"],"created_at":"2024-10-12T06:42:37.398Z","updated_at":"2025-03-12T02:23:39.870Z","avatar_url":"https://github.com/olegs.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Bioinformatics\n\nReviews on different NGS data analysis methods. \nLaTeX Beamer format.\n\n### Content\n* [atacseq](https://github.com/olegs/bioinformatics/blob/master/atacseq/pipeline.pdf) - summary on ATAC-Seq processing methods\n* [chipseq](https://github.com/olegs/bioinformatics/blob/master/chipseq/chipseq.pdf) - summary on ChIP-Seq processing from qc to replicated peak calling\n* [differential_chipseq](https://github.com/olegs/bioinformatics/blob/master/differential_chipseq/diffchipseq.pdf) - how to compare replicated data\n* [peaks](https://github.com/olegs/bioinformatics/blob/master/peaks/peaks.pdf) - notes on peaks classification by length based on small subset of [Roadmap Epigenomics](http://www.roadmapepigenomics.org/) data \n\n### ENCODE resources\nENCODE standards \u003chttps://www.encodeproject.org/data-standards\u003e  \nENCODE Rest API \u003chttps://www.encodeproject.org/help/rest-api\u003e  \nENCODE DNANexus pipelines source \u003chttps://github.com/ENCODE-DCC\u003e  \n\n### Others\nChIP-seq analysis notes from Tommy Tang \u003chttps://github.com/crazyhottommy/ChIP-seq-analysis\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Folegs%2Fbioinformatics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Folegs%2Fbioinformatics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Folegs%2Fbioinformatics/lists"}