{ "_id": "6a516a5f9b92047c28d50802", "Package": "scTenifoldKnk", "Type": "Package", "Title": "In-Silico Knockout Experiments from Single-Cell Gene Regulatory\nNetworks", "Version": "1.1", "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": "2026-07-10 21:16:13 UTC", "RemoteUrl": "https://github.com/cailab-tamu/sctenifoldknk", "RemoteRef": "HEAD", "RemoteSha": "d635a5855295b4ee75909438b09b2ea27ce3437c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-10 21:52:06 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. Cai [aut, ctb, ths] (ORCID:\n)", "Maintainer": "Daniel Osorio ", "_user": "cailab-tamu", "_type": "src", "_file": "scTenifoldKnk_1.1.tar.gz", "_fileid": "https://r2.ropensci.org/9451df41a11e25469b086558a0b2ddc10eec3e5e4e808bb2f0587b3b57cd521c", "_filesize": 246644, "_sha256": "9451df41a11e25469b086558a0b2ddc10eec3e5e4e808bb2f0587b3b57cd521c", "_expires": "2026-10-18T21:55:41.000Z", "_created": "2026-07-10T21:52:06.000Z", "_published": "2026-07-10T21:55:43.037Z", "_jobs": [ { "job": 86471771212, "time": 172, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8240362802" }, { "job": 86471771222, "time": 166, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8240361060" }, { "job": 86471771226, "time": 123, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8240349253" }, { "job": 86471771214, "time": 96, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8240341840" }, { "job": 86471116838, "time": 251, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8240312742" }, { "job": 86471771191, "time": 129, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8240350825" }, { "job": 86471771245, "time": 113, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8240347711" }, { "job": 86471771293, "time": 119, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8240348257" }, { "job": 86471771408, "time": 124, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8240350138" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/29125825023", "_status": "success", "_upstream": "https://github.com/cailab-tamu/sctenifoldknk", "_commit": { "id": "d635a5855295b4ee75909438b09b2ea27ce3437c", "author": "Daniel Osorio ", "committer": "Daniel Osorio ", "message": "Bump version to 1.1 and specify minimum required version for scTenifoldNet\n", "time": 1783718173 }, "_maintainer": { "name": "Daniel Osorio", "email": "dcosorioh@gmail.com", "orcid": "0000-0003-4424-8422" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "scTenifoldNet", "version": ">= 1.4", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "enrichR", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" } ], "_owner": "cailab-tamu", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-38", "n": 1 }, { "week": "2026-04", "n": 1 }, { "week": "2026-05", "n": 1 }, { "week": "2026-15", "n": 1 }, { "week": "2026-18", "n": 4 }, { "week": "2026-28", "n": 3 } ], "_tags": [ { "name": "v.1.0.3", "date": "2026-01-23" } ], "_topics": [ "functional-genomics", "gene-function", "gene-knockout", "gene-regulatory-network", "virtual-knockout-experiments" ], "_stars": 267, "_contributors": [ { "user": "jamesjcai", "count": 27, "uuid": 3751222 }, { "user": "dosorio", "count": 15, "uuid": 1197740 }, { "user": "yanzhong07", "count": 2, "uuid": 48918062 }, { "user": "qianxu05172019", "count": 1, "uuid": 58751639 }, { "user": "yjgeno", "count": 1, "uuid": 77600778 } ], "_userbio": { "uuid": 31963060, "type": "organization", "name": "Cai Lab at Texas A&M (cailab-tamu)", "followers": 33, "description": "Single-Cell Biology / Machine Learning / Quantum Computing" }, "_downloads": { "count": 2059, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/scTenifoldKnk" }, "_devurl": "https://github.com/cailab-tamu/sctenifoldknk", "_searchresults": 53, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/scTenifoldKnk.html", "manual.pdf" ], "_homeurl": "https://github.com/cailab-tamu/sctenifoldknk", "_realowner": "cailab-tamu", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2020-11-23" }, { "version": "1.0.1", "date": "2021-01-22" }, { "version": "1.0.3", "date": "2026-01-25" } ], "_exports": [ "dRegulation", "plotKO", "scQC", "scTenifoldKnk" ], "_help": [ { "page": "dRegulation", "title": "Evaluates gene differential regulation based on manifold alignment distances.", "topics": [ "dRegulation" ] }, { "page": "plotKO", "title": "Plot KO network", "topics": [ "plotKO" ] }, { "page": "scQC", "title": "Performs single-cell data quality control", "topics": [ "scQC" ] }, { "page": "scTenifoldKnk", "title": "scTenifoldKNK", "topics": [ "scTenifoldKnk" ] } ], "_readme": "https://github.com/cailab-tamu/sctenifoldknk/raw/HEAD/README.md", "_rundeps": [ "askpass", "cli", "codetools", "cpp11", "curl", "digest", "enrichR", "farver", "furrr", "future", "ggplot2", "globals", "glue", "gtable", "httr", "igraph", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "listenv", "magrittr", "MASS", "Matrix", "mime", "openssl", "parallelly", "pkgconfig", "plyr", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "reshape2", "RhpcBLASctl", "rjson", "rlang", "RSpectra", "S7", "scales", "scTenifoldNet", "stringi", "stringr", "sys", "vctrs", "viridisLite", "withr", "WriteXLS" ], "_score": 7.54362472363102, "_indexed": true, "_nocasepkg": "sctenifoldknk", "_universes": [ "cailab-tamu" ], "_previous": "1.0.3", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1", "date": "2026-07-10T21:54:41.000Z", "distro": "resolute", "commit": "d635a5855295b4ee75909438b09b2ea27ce3437c", "fileid": "https://r2.ropensci.org/496172c939df8d5000c8da1b1576143778320128e2b4a2c51e3379a6adbd8267", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/29125825023" }, { "r": "4.6.1", "os": "linux", "version": "1.1", "date": "2026-07-10T21:54:38.000Z", "distro": "resolute", "commit": "d635a5855295b4ee75909438b09b2ea27ce3437c", "fileid": "https://r2.ropensci.org/7bc67252652f4de4414fc80bee05964e9cf9f17dddd560b93063a5bbea0346ed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/29125825023" }, { "r": "4.5.3", "os": "mac", "version": "1.1", "date": "2026-07-10T21:54:00.000Z", "commit": "d635a5855295b4ee75909438b09b2ea27ce3437c", "fileid": "https://r2.ropensci.org/ee78d002a71d75b4f37de1a8cb1ab5518b625be189f1525c7647f436b0bf5277", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/29125825023" }, { "r": "4.6.1", "os": "mac", "version": "1.1", "date": "2026-07-10T21:53:39.000Z", "commit": "d635a5855295b4ee75909438b09b2ea27ce3437c", "fileid": "https://r2.ropensci.org/95fad7f3b33fd601d946c1d5bd1bc9c754332323c983f7741ce6ec75c6688763", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/29125825023" }, { "r": "4.6.0", "os": "wasm", "version": "1.1", "date": "2026-07-10T21:54:35.000Z", "commit": "d635a5855295b4ee75909438b09b2ea27ce3437c", "fileid": "https://r2.ropensci.org/0959bca4075ef884aeb7ebe6ae2621e5e72eb4646fc5a7b569a4a0b404210ef4", "status": "success", "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/29125825023" }, { "r": "4.7.0", "os": "win", "version": "1.1", "date": "2026-07-10T21:53:41.000Z", "commit": "d635a5855295b4ee75909438b09b2ea27ce3437c", "fileid": "https://r2.ropensci.org/d0153caf573bea6d3f075f3a9d13f645b8e0d766d725d92e636499a6f64a0e9b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/29125825023" }, { "r": "4.5.3", "os": "win", "version": "1.1", "date": "2026-07-10T21:53:44.000Z", "commit": "d635a5855295b4ee75909438b09b2ea27ce3437c", "fileid": "https://r2.ropensci.org/34fce528322e6d1106db6403d78667bf76272ef26ef085aaf94cc33b58c9771b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/29125825023" }, { "r": "4.6.1", "os": "win", "version": "1.1", "date": "2026-07-10T21:53:54.000Z", "commit": "d635a5855295b4ee75909438b09b2ea27ce3437c", "fileid": "https://r2.ropensci.org/3fabaa87a3ee21f72f7530c0cc4a15975ede788654229d359c6a962529f17651", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cailab-tamu/actions/runs/29125825023" } ] }