{"id":28436068,"url":"https://github.com/immunogenomics/gena","last_synced_at":"2025-10-25T10:44:39.552Z","repository":{"id":191702151,"uuid":"685209111","full_name":"immunogenomics/GeNA","owner":"immunogenomics","description":"Genotype-Neighborhood Associations:  A tool for identifying genetic variant associations to the abundance of cell states in single-cell datasets","archived":false,"fork":false,"pushed_at":"2024-10-05T15:02:54.000Z","size":78873,"stargazers_count":14,"open_issues_count":0,"forks_count":1,"subscribers_count":11,"default_branch":"main","last_synced_at":"2025-06-05T21:09:55.315Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","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":"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":"2023-08-30T18:34:15.000Z","updated_at":"2025-04-29T00:02:22.000Z","dependencies_parsed_at":"2023-08-31T08:38:39.338Z","dependency_job_id":"d485dda9-195d-4bff-b129-e7820516076e","html_url":"https://github.com/immunogenomics/GeNA","commit_stats":null,"previous_names":["immunogenomics/gena"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/immunogenomics/GeNA","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2FGeNA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2FGeNA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2FGeNA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2FGeNA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/immunogenomics","download_url":"https://codeload.github.com/immunogenomics/GeNA/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2FGeNA/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262311003,"owners_count":23291663,"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":"2025-06-05T21:10:01.523Z","updated_at":"2025-10-25T10:44:39.548Z","avatar_url":"https://github.com/immunogenomics.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# GeNA\n`GeNA` (Genotype-Neighborhood Associations) is a tool for identifying genetic variant associations to the abundance of cell states in single-cell datasets (cell state abundance quantitative trait loci, csaQTLs). In `GeNA`, we have adapted the framework we developed for [Covarying Neighborhood Analysis](https://github.com/immunogenomics/cna) in order to enable genome-wide csaQTL surveys in single-cell data. Instead of testing associations to predefined cell types, `GeNA` identifies the granular cell states whose abundance is most associated with genetic variants. The scripts required to run `GeNA` are stored in this repo.\n\nWe have evaluated GeNA in simulation to assess calibration and statistical power and we have applied `GeNA` in a genome-wide survey to scRNA-seq profiling from a cohort of 969 individuals. Scripts documenting our use of `GeNA` in these analyses for our manuscript are found in a separate repository, [immunogenomics/GeNA-applied](https://github.com/immunogenomics/GeNA-applied/).\n\n# Installation\nTo use `GeNA`, you can clone this repository.\nDependencies:\n- Python version 3.8.10\n- R version 4.1.1\n- PLINK version 2.00a2.3\n- CNA version 0.1.6\n- Rmpfr version 0.8-7\n\n# Tutorial\nWe illustrate how to use `GeNA` in a tutorial [here](https://github.com/immunogenomics/GeNA/blob/main/tutorial/Example_csaQTL_GWAS.ipynb). First, we demonstrate how to construct the single-cell data object format `GeNA` expects, then we summarize the arguments input to and files output from a call to `GeNA`. Finally, we illustrate basic characterization of example loci.\n\n# Citation\nIf you use `GeNA` in your work, you can cite our paper [here](https://www.nature.com/articles/s41588-024-01909-1)\n\n# Contact\nIf you have questions about `GeNA` or require user support, please contact Laurie Rumker (Laurie_Rumker AT hms.harvard.edu) or post an issue on this repo.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fimmunogenomics%2Fgena","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fimmunogenomics%2Fgena","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fimmunogenomics%2Fgena/lists"}