{"id":19749609,"url":"https://github.com/mskcc/immunosarc","last_synced_at":"2026-05-11T21:34:51.541Z","repository":{"id":75108394,"uuid":"469773735","full_name":"mskcc/ImmunoSarc","owner":"mskcc","description":null,"archived":false,"fork":false,"pushed_at":"2022-03-15T17:02:35.000Z","size":627,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-02-28T08:28:48.712Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":false,"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/mskcc.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}},"created_at":"2022-03-14T14:39:35.000Z","updated_at":"2022-03-15T17:02:39.000Z","dependencies_parsed_at":"2023-06-05T09:15:20.601Z","dependency_job_id":null,"html_url":"https://github.com/mskcc/ImmunoSarc","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/mskcc/ImmunoSarc","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FImmunoSarc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FImmunoSarc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FImmunoSarc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FImmunoSarc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/ImmunoSarc/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FImmunoSarc/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32913942,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-11T17:09:15.040Z","status":"ssl_error","status_checked_at":"2026-05-11T17:08:45.420Z","response_time":120,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":"2024-11-12T02:27:25.251Z","updated_at":"2026-05-11T21:34:51.524Z","avatar_url":"https://github.com/mskcc.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ImmunoSarc\n\n\n\n## Figures\nFigures directory includes source data and code necessary to recreate all figures and supplemental figures.\n\n## GeneralProcessing\nGeneralProcessing directory includes scripts used for processing and overall analysis of the data.\n\nScripts to process RNA-seq are found in GeneralProcessing and include:\n\n```\nRunSTAR.sh\nRunKallisto.sh\nRunFusionCatcher.sh\nRunArriba.sh\nCombineFusionCalls.R\n```\n\nFurther information on references and versions can be found in the Methods section of the manuscript.\n\nOther GeneralProcessing scripts require output from Tempo (for WES), Kallisto and above scripts (for RNA-seq) and MiXCR and VDJtools (for TCR-seq), as well as patient and sample data that are provided in the Figures directory or in supplemental material.\n\nSetUpData.R - Script to organize data and identify Immune groups. This script also includes a heatmap similar to Figure 2D and 2E except missing a handful of tracks.\n\nCompareVariablesToResponseAndCohort.R - Script to recreate plots and p-values for figures comparing variables (e.g. IHC values, TCR diversity, TMB, etc) to sample cohort or patient response. Relevant to Figure 2, and supplemental figures 2, 3, 5, and 6.\n\nKMPlots.R - Script on Kaplan-Meier plots and how we compare survival. Relevant to Figure 2, and supplemental figures 1, 5 and 6.\n\nSleuth_Prep_Run.R - Script for running sleuth_prep.\n\nDifferentialExpressionAnalysis.R - Script describing the differential expression analysis, gene set enrichment analysis and modeling included in Figure 3 and supplemental figure 3.\n\n## Contact\nE-mail any questions to richara4@mskcc.org.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fimmunosarc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Fimmunosarc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fimmunosarc/lists"}