{ "_id": "6a116606acfb0bcc41cf07e5", "Package": "scTenifoldKnk", "Type": "Package", "Title": "In-Silico Knockout Experiments from Single-Cell Gene Regulatory\nNetworks", "Version": "2.1.0", "Author": "Zaoqu Liu [ctb, cre], Daniel Osorio [aut], Yan Zhong [aut,\nctb], Guanxun Li [aut, ctb], Qian Xu [aut, ctb], Andrew\nHillhouse [aut, ctb], Jingshu Chen [aut, ctb], Laurie Davidson\n[aut, ctb], Yanan Tian [aut, ctb], Robert Chapkin [aut, ctb],\nJianhua Huang [aut, ctb], James Cai [aut, ctb, ths]", "Maintainer": "Zaoqu Liu ", "Authors@R": "c(person(given = \"Zaoqu\", family = \"Liu\", email = \"liuzaoqu@163.com\", role = c(\"ctb\", \"cre\"), comment = c(ORCID = '0000-0002-0452-742X')),\nperson(given = \"Daniel\", family = \"Osorio\", email = \"dcosorioh@tamu.edu\", role = c(\"aut\"), 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 = \"Andrew\", family = \"Hillhouse\", role = c(\"aut\",\"ctb\")),\nperson(given = \"Jingshu\", family = \"Chen\", role = c(\"aut\",\"ctb\")),\nperson(given = \"Laurie\", family = \"Davidson\", 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\", 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. This version includes C++ acceleration with\nEigen library, cross-platform compatibility (macOS, Linux,\nWindows), and Seurat v4/v5 support.", "URL": "https://zaoqu-liu.github.io/scTenifoldKnk/,\nhttps://github.com/Zaoqu-Liu/scTenifoldKnk", "BugReports": "https://github.com/Zaoqu-Liu/scTenifoldKnk/issues", "License": "GPL (>= 2)", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "SystemRequirements": "GNU make", "NeedsCompilation": "yes", "Config/pak/sysreqs": "make", "Repository": "https://zaoqu-liu.r-universe.dev", "Date/Publication": "2026-01-23 08:35:24 UTC", "RemoteUrl": "https://github.com/Zaoqu-Liu/scTenifoldKnk", "RemoteRef": "HEAD", "RemoteSha": "08118337f6fc22cca5a22c443ccb78ef920dfa3b", "Packaged": { "Date": "2026-05-23 08:26:32 UTC", "User": "root" }, "MD5sum": "db6c6853c7473ff01d9a7be8e1a5eb9c", "_user": "zaoqu-liu", "_type": "src", "_file": "scTenifoldKnk_2.1.0.tar.gz", "_fileid": "7e543cdb3fc1e70a4d5708439a5a11602ebf0554fa115462ee0c70741c607028", 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