{ "_id": "6a106ac8acfb0bcc41caa1d1", "Package": "NTW", "Type": "Package", "Title": "Predict gene network using an Ordinary Differential Equation\n(ODE) based method", "Version": "1.63.0", "Date": "2011-10-8", "Author": "Wei Xiao, Yin Jin, Darong Lai, Xinyi Yang, Yuanhua Liu,\nChristine Nardini", "Maintainer": "Yuanhua Liu ", "Description": "This package predicts the gene-gene interaction network\nand identifies the direct transcriptional targets of the\nperturbation using an ODE (Ordinary Differential Equation)\nbased method.", "License": "GPL-2", "biocViews": "Preprocessing", "LazyLoad": "yes", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:34:43 UTC", "RemoteUrl": "https://github.com/bioc/NTW", "RemoteRef": "HEAD", "RemoteSha": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-07 09:43:35 UTC", "User": "root" }, "MD5sum": "6e215b01599c5d8cebed963ff86474b2", "_user": "bioc", "_type": "src", "_file": "NTW_1.63.0.tar.gz", "_fileid": "d24635997befb5ded15e3a6ebe5f636a8df3dce99258add2c84817b8c37e1c9e", "_filesize": 882040, "_sha256": "d24635997befb5ded15e3a6ebe5f636a8df3dce99258add2c84817b8c37e1c9e", "_created": "2026-05-07T09:43:35.000Z", "_published": "2026-05-22T14:40:08.198Z", "_jobs": [ { "job": 77402123800, "time": 130, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "6851904083" }, { "job": 77402123740, "time": 131, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "6851904910" }, { "job": 77402124131, "time": 155, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "6851912713" }, { "job": 77402123681, "time": 102, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "6851893930" }, { "job": 77402123623, "time": 91, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "6851889861" }, { "job": 77402122972, "time": 136, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6851859753" }, { "job": 77402123218, "time": 88, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7163206890" }, { "job": 77402123794, "time": 68, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "6851882678" }, { "job": 77402123957, "time": 73, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "6851884458" }, { "job": 77402123860, "time": 80, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "6851886428" } ], "_bioccheck": { "error": 2, "warning": 2, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25488188757", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/NTW", "_commit": { "id": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379683 }, "_maintainer": { "name": "Yuanhua Liu", "email": "liuyuanhua@picb.ac.cn" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.3.0", "role": "Depends" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.63.0", "bioc": "3.24" }, { "branch": "release", "version": "1.62.0", "bioc": "3.23" } ], "_topics": [ "preprocessing" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 336, "source": "https://www.bioconductor.org/packages/stats/bioc/NTW" }, "_mentions": 3, "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/NTW.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "A.estimation.Srow", "AP.estimation.Srow", "backward", "comb.matrix", "forward", "method.geo", "method.ml", "method.sse", "NTW", "P.preestimation" ], "_datasets": [ { "name": "sos.data", "title": "SOS pathway perturbation data", "object": "sos.data", "file": "sos.data.rda", "class": [ "data.frame" ], "fields": [ "p.recA", "p.lexA", "p.ssb", "p.recF", "p.dinI", "p.umuDC", "p.rpoD", "p.rpoH", "p.rpoS" ], "rows": 9, "table": true, "tojson": true } ], "_help": [ { "page": "NTW-package", "title": "Gene interaction network and perturbation targets predictions", "topics": [ "NTW-package" ] }, { "page": "A.estimation.Srow", "title": "Estimation of a single row in matrix A with the perturbation targets matrix P known", "topics": [ "A.estimation.Srow" ] }, { "page": "AP.estimation.Srow", "title": "Estimation of a single row in gene interaction matrix A and perturbation targets matrix P", "topics": [ "AP.estimation.Srow" ] }, { "page": "comb.matrix", "title": "Create all combinations of vectors", "topics": [ "comb.matrix" ] }, { "page": "methods.regression", "title": "Regression methods to estimate a single row in A with fixed perturbations", "topics": [ "method.geo", "method.ml", "method.sse" ] }, { "page": "NTW", "title": "Estimation of gene interaction matrix A and perturbation targets matrix P", "topics": [ "NTW" ] }, { "page": "P.preestimation", "title": "Pre-estimation of the transcriptional pertubation targets matrix P", "topics": [ "P.preestimation" ] }, { "page": "patterns.priorA", "title": "Approaches to use a priori known gene association information for a single row estimation in matrix A", "topics": [ "backward", "forward" ] }, { "page": "sos.data", "title": "SOS pathway perturbation data", "topics": [ "sos.data" ] } ], "_rundeps": [ "mvtnorm" ], "_vignettes": [ { "source": "NTW.Rnw", "filename": "NTW.pdf", "title": "NTW vignette", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:13:51", "modified": "2013-11-01 20:13:51", "commits": 1 } ], "_score": 3.778151250383644, "_indexed": true, "_nocasepkg": "ntw", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.63.0", "date": "2026-05-07T09:45:50.000Z", "distro": "noble", "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3", "fileid": "72f42ac95520d59faf48fc337a91d408bc6d8663ccad50d8020af25b9d818bf9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25488188757" }, { "r": "4.6.0", "os": "linux", "version": "1.63.0", "date": "2026-05-07T09:46:17.000Z", "distro": "noble", "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3", "fileid": "6412def11967780fc1b0a384750105b8c1e76340e0fbf4656c32056dc75aeaec", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25488188757" }, { "r": "4.5.3", "os": "mac", "version": "1.63.0", "date": "2026-05-07T09:45:19.000Z", "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3", "fileid": "dc2facfc5818f5eaa56e5d2c7885579ae907d55663e1497761ffc9604d23b856", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25488188757" }, { "r": "4.6.0", "os": "mac", "version": "1.63.0", "date": "2026-05-07T09:45:06.000Z", "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3", "fileid": "287a0e329fb0344bfaffb867d774c83b7a1eb623ec489296f108a2562d281f9a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25488188757" }, { "r": "4.7.0", "os": "win", "version": "1.63.0", "date": "2026-05-07T09:44:37.000Z", "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3", "fileid": "8fdfde02676765daa658b8a20bedc4e162a6a9bd1efbd4a05f4b9e21646956ae", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25488188757" }, { "r": "4.5.3", "os": "win", "version": "1.63.0", "date": "2026-05-07T09:44:42.000Z", "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3", "fileid": "fc0bfc0931d8dad6d36201e8656ffd4b9cecdf0b19a32e45fd54dd445b626996", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25488188757" }, { "r": "4.6.0", "os": "win", "version": "1.63.0", "date": "2026-05-07T09:44:48.000Z", "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3", "fileid": "90dff5a46dffab9697d4d9dff0bea5a2acb3a469a90dfa396933e27c5cafe6b3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25488188757" }, { "r": "4.6.0", "os": "wasm", "version": "1.63.0", "date": "2026-05-22T14:39:53.000Z", "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3", "fileid": "f5eb9b16953af63e12a401d435bafbbe8e66c37119e9c75f7c33611251f7711e", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25488188757" } ] }