{"id":20425047,"url":"https://github.com/databio/lolahema_pep","last_synced_at":"2026-04-19T02:33:17.654Z","repository":{"id":86287789,"uuid":"216650174","full_name":"databio/LOLAHema_PEP","owner":"databio","description":"Portable Encapsulated Project for the LOLAHema database. ","archived":false,"fork":false,"pushed_at":"2021-10-09T22:57:56.000Z","size":171,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-09-11T10:15:38.781Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","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/databio.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-10-21T19:34:47.000Z","updated_at":"2021-10-09T22:57:58.000Z","dependencies_parsed_at":"2023-03-13T09:28:31.242Z","dependency_job_id":null,"html_url":"https://github.com/databio/LOLAHema_PEP","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/databio/LOLAHema_PEP","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FLOLAHema_PEP","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FLOLAHema_PEP/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FLOLAHema_PEP/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FLOLAHema_PEP/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/databio","download_url":"https://codeload.github.com/databio/LOLAHema_PEP/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FLOLAHema_PEP/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31992001,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-18T20:23:30.271Z","status":"online","status_checked_at":"2026-04-19T02:00:07.110Z","response_time":55,"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":"2024-11-15T07:12:07.589Z","updated_at":"2026-04-19T02:33:17.627Z","avatar_url":"https://github.com/databio.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# LOLAHema_PEP\nPortable Encapsulated Project (PEP) for the LOLAHema database.  \n\nThis [PEP](http://pep.databio.org/en/latest/) is specifically designed to encompass public AML relevant samples. The PEP sample sheet and config files can be accessed directly with the following links:\n- [Sample sheet](https://github.com/databio/LOLAHema_PEP/blob/master/LOLAHema_samples.csv)\n- [YAML Config file](https://github.com/databio/LOLAHema_PEP/blob/master/LOLAHema_samples_cfg.yaml) \n\nThe .csv sample sheet contains the following attributes for each of the files:  \n\n- **sample_name**\n- **file_name**\n- **genome**\n- **experimental protocol**\n- cell type\n- tissue\n- antibody\n- treatment\n- data_source\n- GSE\n- GSM\n- description\n- file format\n\n\nThe attributes highlighted in bold are used to create derived attributes such as `output_file_path` which points to the location of the BED files produced by the [bedmaker](https://github.com/databio/bedmaker) pipeline (please take a look at the config file). Accordingly, samples in this PEP can be easily processed with other PEP compatible pipelines such as [bedstat](https://github.com/databio/bedstat) and [bedbuncher](https://github.com/databio/bedbuncher). \n\nThere is an additional PEP ([lifOver_PEP](https://github.com/databio/LOLAHema_PEP/tree/master/liftOver_PEPs)) in the repository that contains files that have been liftedOver to different reference genome assemblies (e.g., hg19 to hg38).    \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Flolahema_pep","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabio%2Flolahema_pep","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Flolahema_pep/lists"}