{"id":28436033,"url":"https://github.com/immunogenomics/amp_phase1_ra_viewer","last_synced_at":"2025-06-27T18:31:36.707Z","repository":{"id":80827409,"uuid":"119050269","full_name":"immunogenomics/amp_phase1_ra_viewer","owner":"immunogenomics","description":"🌻 View single-cell RNA-seq and mass cytometry data in synovial tissues from patients with RA or OA.","archived":false,"fork":false,"pushed_at":"2019-06-18T01:45:17.000Z","size":1252,"stargazers_count":4,"open_issues_count":5,"forks_count":2,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-06-05T21:09:47.333Z","etag":null,"topics":["cytof-data","data-science","data-visualization","r","rna-seq-data","shiny-apps","single-cell-rna-seq"],"latest_commit_sha":null,"homepage":"https://immunogenomics.io/ampra","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}},"created_at":"2018-01-26T12:42:24.000Z","updated_at":"2025-03-05T09:12:30.000Z","dependencies_parsed_at":null,"dependency_job_id":"0fb13e05-8fbf-46f2-9cc5-d82df7dc4c66","html_url":"https://github.com/immunogenomics/amp_phase1_ra_viewer","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/immunogenomics/amp_phase1_ra_viewer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2Famp_phase1_ra_viewer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2Famp_phase1_ra_viewer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2Famp_phase1_ra_viewer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2Famp_phase1_ra_viewer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/immunogenomics","download_url":"https://codeload.github.com/immunogenomics/amp_phase1_ra_viewer/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/immunogenomics%2Famp_phase1_ra_viewer/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262310888,"owners_count":23291639,"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":["cytof-data","data-science","data-visualization","r","rna-seq-data","shiny-apps","single-cell-rna-seq"],"created_at":"2025-06-05T21:09:55.638Z","updated_at":"2025-06-27T18:31:36.639Z","avatar_url":"https://github.com/immunogenomics.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# amp_phase1_ra_viewer \u003ca href=\"https://github.com/immunogenomics\"\u003e\u003cimg src=\"https://avatars3.githubusercontent.com/u/13906712\" width=\"121px\" align=\"right\" /\u003e\u003c/a\u003e\n\nAn app for viewing single-cell RNA-seq and mass cytometry data in synovial tissues from RA and OA patients.\n\n## :rocket: Explore the data\n\n\u003cp align=\"center\"\u003e\n  \u003cb\u003ehttps://immunogenomics.io/ampra\u003c/b\u003e\n  \u003ca href=\"https://immunogenomics.io/ampra/\"\u003e\u003cimg width=\"80%\" src=\"screenshot.jpg\"\u003e\u003c/a\u003e\n\u003c/p\u003e\n\n## :mortar_board: Read the paper\n\n**Defining Inflammatory Cell States in Rheumatoid Arthritis Joint Synovial Tissues by Integrating Single-cell Transcriptomics and Mass Cytometry**\n\nFan Zhang, Kevin Wei, Kamil Slowikowski, Chamith Y. Fonseka, Deepak A. Rao, Stephen Kelly, Susan M. Goodman, Darren Tabechian, Laura B. Hughes, Karen Salomon-Escoto, Gerald F. M. Watts, William Apruzzese, David J. Lieb, David L. Boyle, Arthur M. Mandelin II, Accelerating Medicines Partnership: RA Phase 1, AMP RA/SLE, Brendan F. Boyce, Edward DiCarlo, Ellen M. Gravallese, Peter K. Gregersen, Larry Moreland, Gary S. Firestein, Nir Hacohen, Chad Nusbaum, James A. Lederer, Harris Perlman, Costantino Pitzalis, Andrew Filer, V. Michael Holers, Vivian P. Bykerk, Laura T. Donlin, Jennifer H. Anolik, Michael B. Brenner, Soumya Raychaudhuri\n\n*Nature Immunology* 2019. https://doi.org/10.1038/s41590-019-0378-1\n\n## :floppy_disk: Get the data\n\nDownload the data from ImmPort:\n\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"http://www.immport.org/immport-open/public/study/study/displayStudyDetail/SDY998\"\u003eSDY998:\nAMP Rheumatoid Arthritis Phase 1\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\n## :octocat: Get the code\n\nGet the code for the analysis in the paper:\n\n- https://github.com/immunogenomics/amp_phase1_ra\n\nGet the code for the data viewer:\n\n- https://github.com/immunogenomics/amp_phase1_ra_viewer\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fimmunogenomics%2Famp_phase1_ra_viewer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fimmunogenomics%2Famp_phase1_ra_viewer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fimmunogenomics%2Famp_phase1_ra_viewer/lists"}