{ "_id": "6a17de97acfb0bcc41d9d003", "Package": "scTenifoldKnk", "Type": "Package", "Title": "In-Silico Knockout Experiments from Single-Cell Gene Regulatory\nNetworks", "Version": "1.0.3", "Authors@R": "c(person(given = \"Daniel\", family = \"Osorio\", email = \"dcosorioh@gmail.com\", role = c(\"aut\",\"cre\"), comment = c(ORCID = '0000-0003-4424-8422')),\nperson(given = \"Yan\", family = \"Zhong\", role = c(\"aut\",\"ctb\")),\nperson(given = \"Guanxun\", family = \"Li\", role = c(\"aut\",\"ctb\")),\nperson(given = \"Qian\", family = \"Xu\", role = c(\"aut\",\"ctb\")),\nperson(given = \"Yongjian\", family = \"Yang\", role = c(\"aut\",\"ctb\")),\nperson(given = \"Yanan\", family = \"Tian\", role = c(\"aut\",\"ctb\")),\nperson(given = \"Robert\", family = \"Chapkin\", role = c(\"aut\",\"ctb\")),\nperson(given = \"Jianhua\", family = \"Huang\", role = c(\"aut\",\"ctb\")),\nperson(given = \"James J.\", family = \"Cai\", role = c(\"aut\", \"ctb\", \"ths\"), comment = c(ORCID = '0000-0002-8081-6725'))\n)", "Description": "A workflow based on 'scTenifoldNet' to perform in-silico\nknockout experiments using single-cell RNA sequencing\n(scRNA-seq) data from wild-type (WT) control samples as input.\nFirst, the package constructs a single-cell gene regulatory\nnetwork (scGRN) and knocks out a target gene from the adjacency\nmatrix of the WT scGRN by setting the gene’s outdegree edges to\nzero. Then, it compares the knocked out scGRN with the WT scGRN\nto identify differentially regulated genes, called\nvirtual-knockout perturbed genes, which are used to assess the\nimpact of the gene knockout and reveal the gene’s function in\nthe analyzed cells.", "URL": "https://github.com/cailab-tamu/scTenifoldKnk", "BugReports": "https://github.com/cailab-tamu/scTenifoldKnk/issues", "License": "GPL (>=2)", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "biocViews": "", "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev libssl-dev perl", "Repository": "https://cailab-tamu.r-universe.dev", "Date/Publication": "2026-04-28 14:15:54 UTC", "RemoteUrl": "https://github.com/cailab-tamu/sctenifoldknk", "RemoteRef": "HEAD", "RemoteSha": "5232d9eaba4e5e59886c40eac67dc4021246cad8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 06:15:54 UTC", "User": "root" }, "Author": "Daniel Osorio [aut, cre] (ORCID:\n),\nYan Zhong [aut, ctb],\nGuanxun Li [aut, ctb],\nQian Xu [aut, ctb],\nYongjian Yang [aut, ctb],\nYanan Tian [aut, ctb],\nRobert Chapkin [aut, ctb],\nJianhua Huang [aut, ctb],\nJames J. 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