{"id":51002649,"url":"https://github.com/databio/renin_atac","last_synced_at":"2026-06-20T16:32:42.974Z","repository":{"id":335153576,"uuid":"1057589967","full_name":"databio/renin_atac","owner":"databio","description":null,"archived":false,"fork":false,"pushed_at":"2026-01-28T19:16:33.000Z","size":4890,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2026-03-01T17:11:21.696Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-09-16T00:10:48.000Z","updated_at":"2026-01-28T19:16:37.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/databio/renin_atac","commit_stats":null,"previous_names":["databio/renin_atac"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/databio/renin_atac","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Frenin_atac","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Frenin_atac/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Frenin_atac/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Frenin_atac/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/databio","download_url":"https://codeload.github.com/databio/renin_atac/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Frenin_atac/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34578089,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-20T02:00:06.407Z","response_time":98,"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":"2026-06-20T16:32:41.647Z","updated_at":"2026-06-20T16:32:42.970Z","avatar_url":"https://github.com/databio.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Renin cell identity\n\nHere we include a step-by-step breakdown of the analyses to reproduce the data presented in \"The reninness score: integrative analysis of multi-omic data to define renin cell identity\".\n\nThe goal is to identify a unique epigenetic landscape that defines renin cell identity; and develop a computational tool to use that unique epigenetic landscape to identify renin-expressing cells, and quantify the renin program of unknown cell samples. \n\n## Overview of the experimental design\n![workflow](img/concept.svg)\n\n## Read preprocessing \nWe used the PEPATAC pipeline to process the raw ATAC-seq reads, including alignment, peak-calling, and quality control.  The input files to run PEPATAC for this study are stored in the [metadata](metadata) sub-folder. For more information on how to use PEPATAC, see: http://pepatac.databio.org/\n\n## Consensus peak set generation\nWe used the genomic interval machine learning (geniml) Python package to construct a consensus region set, or the “universe”, using maximum likelihood approach. For more information on how to use `genimal`, see: https://docs.bedbase.org/geniml/tutorials/create-consensus-peaks/\n\n## Differential accessibility analysis and differential accessibile region annotation\nAll code used for differential accessibility analysis and differential accessibile region annotation are stored in the [src](src) sub-folder.\n\n## Reninness score calculation and model performace evaluation\nAll code used for model training and reninness score calulation can be found [here](https://github.com/databio/reninness_score/tree/master)). All code used for model performace evaluation are stored in the [src](src) sub-folder.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Frenin_atac","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabio%2Frenin_atac","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Frenin_atac/lists"}