{"id":28436047,"url":"https://github.com/immunogenomics/tb_tcell_citeseq","last_synced_at":"2025-08-18T11:06:18.777Z","repository":{"id":100624059,"uuid":"354967994","full_name":"immunogenomics/TB_Tcell_CITEseq","owner":"immunogenomics","description":"Code for analysis of memory T cell CITE-seq data","archived":false,"fork":false,"pushed_at":"2021-05-11T02:46:56.000Z","size":58,"stargazers_count":6,"open_issues_count":1,"forks_count":4,"subscribers_count":10,"default_branch":"main","last_synced_at":"2025-06-27T18:43:22.287Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","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,"zenodo":null}},"created_at":"2021-04-05T20:45:53.000Z","updated_at":"2025-03-11T06:32:51.000Z","dependencies_parsed_at":"2023-05-16T10:30:21.656Z","dependency_job_id":null,"html_url":"https://github.com/immunogenomics/TB_Tcell_CITEseq","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/immunogenomics/TB_Tcell_CITEseq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2FTB_Tcell_CITEseq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2FTB_Tcell_CITEseq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2FTB_Tcell_CITEseq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2FTB_Tcell_CITEseq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/immunogenomics","download_url":"https://codeload.github.com/immunogenomics/TB_Tcell_CITEseq/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2FTB_Tcell_CITEseq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270982194,"owners_count":24679447,"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","status":"online","status_checked_at":"2025-08-18T02:00:08.743Z","response_time":89,"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":"2025-06-05T21:10:01.100Z","updated_at":"2025-08-18T11:06:18.766Z","avatar_url":"https://github.com/immunogenomics.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CITE-seq of memory T cells from a TB progression cohort\n*TBRU LIMAA*\n\n## Overview\nThis repo provides code used for custom analyses of CITE-seq data from a TB progression cohort at immune steady state to identify a cell state reduced in people who had progressed to active disease. If you are interested in code for any additional analyses from our study, please contact us at aparnanathan@g.harvard.edu\n\nThe published paper can soon be viewed and cited:\n\n\u003e Nathan A, et al, 2021. Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state associations with demographics, environment and disease. [Nature Immunology](https://www.doi.org/10.1038/s41590-021-00933-1), in press.\n\n## Data availability\n\nSingle-cell data are availale on GEO (Accession: GSE158769) and can be interactively browsed on [our website](https://immunogenomics.io/tbru/).\n\nPlease send any questions regarding the study, data, or analyses to Aparna Nathan (aparnanathan@g.harvard.edu).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fimmunogenomics%2Ftb_tcell_citeseq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fimmunogenomics%2Ftb_tcell_citeseq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fimmunogenomics%2Ftb_tcell_citeseq/lists"}