{"id":28436078,"url":"https://github.com/immunogenomics/sc-h2","last_synced_at":"2025-07-21T03:33:16.072Z","repository":{"id":193552095,"uuid":"609676804","full_name":"immunogenomics/sc-h2","owner":"immunogenomics","description":null,"archived":false,"fork":false,"pushed_at":"2023-10-12T15:56:28.000Z","size":33006,"stargazers_count":5,"open_issues_count":0,"forks_count":0,"subscribers_count":11,"default_branch":"main","last_synced_at":"2025-07-07T21:39:00.780Z","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/immunogenomics.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}},"created_at":"2023-03-04T22:27:39.000Z","updated_at":"2024-05-29T12:11:19.000Z","dependencies_parsed_at":"2023-09-26T23:01:22.464Z","dependency_job_id":null,"html_url":"https://github.com/immunogenomics/sc-h2","commit_stats":null,"previous_names":["immunogenomics/sc-h2"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/immunogenomics/sc-h2","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2Fsc-h2","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2Fsc-h2/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2Fsc-h2/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2Fsc-h2/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/immunogenomics","download_url":"https://codeload.github.com/immunogenomics/sc-h2/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2Fsc-h2/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266235439,"owners_count":23897181,"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":[],"created_at":"2025-06-05T21:10:01.792Z","updated_at":"2025-07-21T03:33:16.060Z","avatar_url":"https://github.com/immunogenomics.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Mapping cell state heritability in autoimmunity with single-cell data\n\nCode related to the manuscript \"Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability\" (Accepted in principle at Nature Genetics).\n\nPreprint now available at https://www.medrxiv.org/content/10.1101/2023.02.24.23286364v1\n\nAll scripts required to reproduce the analysis in this paper can also be found at: https://doi.org/10.5281/zenodo.8436010\n\nContact: Anika Gupta anikagupta@g.harvard.edu\n\nTo follow along with the analyses described in the manuscript, we would recommend using the scripts in the following directory order:\n\n1. RNA processing (preparing the counts data for the regressions; also includes a subdirectory with the QC and ATAC processing code)\n2. regressions (underlying basis for this work and the key novelty)\n3. dynamic_peaks_characterization (plots for Figure 2)\n4. stat_gen (preparing the regression outputs for heritability analyses)\n5. ldsc (running heritability enrichment analyses)\n6. h2_post-hoc (making sense of and plotting the heritability outputs; for h2 plots in Figures 3-6)\n7. benchmarking (trying out modified versions of this approach OR the approach as-is but on PBMCs)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fimmunogenomics%2Fsc-h2","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fimmunogenomics%2Fsc-h2","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fimmunogenomics%2Fsc-h2/lists"}