{"id":29625252,"url":"https://github.com/novartis/cellsius","last_synced_at":"2025-07-21T06:07:46.356Z","repository":{"id":72202248,"uuid":"189385961","full_name":"Novartis/CellSIUS","owner":"Novartis","description":"CellSIUS: Cell Subtype Identification from Upregulated gene Sets","archived":false,"fork":false,"pushed_at":"2019-06-03T15:13:42.000Z","size":11561,"stargazers_count":5,"open_issues_count":0,"forks_count":2,"subscribers_count":24,"default_branch":"master","last_synced_at":"2024-04-16T11:10:09.102Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Novartis.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-05-30T09:33:37.000Z","updated_at":"2022-11-07T17:16:52.000Z","dependencies_parsed_at":null,"dependency_job_id":"c806e561-a457-4eff-8ccc-6e4a97856eb2","html_url":"https://github.com/Novartis/CellSIUS","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/Novartis/CellSIUS","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Novartis%2FCellSIUS","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Novartis%2FCellSIUS/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Novartis%2FCellSIUS/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Novartis%2FCellSIUS/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Novartis","download_url":"https://codeload.github.com/Novartis/CellSIUS/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Novartis%2FCellSIUS/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266248501,"owners_count":23899056,"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":"2025-07-21T06:07:45.776Z","updated_at":"2025-07-21T06:07:46.346Z","avatar_url":"https://github.com/Novartis.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CellSIUS: Cell Subtype Identification from Upregulated gene Sets\nCellSIUS is an R package enabling the identification and characterization\nof (rare) cell sub-populations from complex scRNA-seq datasets:\nit takes as input expression values of N cells grouped into M(\u003e1)\nclusters. Within each cluster, genes with a bimodal distribution\nare selected and only genes with cluster-specific expression are\nretained. Among these candidate marker genes, sets with correlated\nexpression patterns are identified by graph-based clustering.\nFinally, cells are assigned to subgroups based on their average\nexpression of each gene set. The CellSIUS algorithm output provides the\nrare/ sub cell types by cell indices and their transcriptomic signatures.\n\n[![DOI](https://zenodo.org/badge/189385961.svg)](https://zenodo.org/badge/latestdoi/189385961)\n\n## Reference\nWegmann *et Al.*, **CellSIUS provides sensitive and specific detection of rare cell populations from complex single cell RNA-seq data**, Genome Biology, 2019 [accepted]\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnovartis%2Fcellsius","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnovartis%2Fcellsius","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnovartis%2Fcellsius/lists"}