{ "_id": "6a1af5a51d7bb097a09f97e5", "Package": "splineTimeR", "Type": "Package", "Title": "Time-course differential gene expression data analysis using\nspline regression models followed by gene association network\nreconstruction", "Version": "1.41.0", "Date": "2020-07-16", "Author": "Agata Michna", "Maintainer": "Herbert Braselmann , Martin\nSelmansberger ", "Description": "This package provides functions for differential gene\nexpression analysis of gene expression time-course data.\nNatural cubic spline regression models are used. Identified\ngenes may further be used for pathway enrichment analysis\nand/or the reconstruction of time dependent gene regulatory\nassociation networks.", "License": "GPL-3", "biocViews": "GeneExpression, DifferentialExpression, TimeCourse,\nRegression, GeneSetEnrichment, NetworkEnrichment,\nNetworkInference, GraphAndNetwork", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Config/pak/sysreqs": "libglpk-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:42:22 UTC", "RemoteUrl": "https://github.com/bioc/splineTimeR", "RemoteRef": "HEAD", "RemoteSha": "69a96090b8963ba8aad4c6722f3a6615365e0a3e", "Packaged": { "Date": "2026-05-30 09:46:50 UTC", "User": "root" }, "MD5sum": "c6a9dd18819f3533f2fa1ffed7a0bbdb", "_user": "bioc", "_type": "src", "_file": "splineTimeR_1.41.0.tar.gz", "_fileid": "9576d58943cdd9eeb780df6f8b59c29f6bb2b1609ba7e98d86ac3f39156776a9", "_filesize": 1276062, "_sha256": "9576d58943cdd9eeb780df6f8b59c29f6bb2b1609ba7e98d86ac3f39156776a9", "_created": "2026-05-30T09:46:50.000Z", "_published": "2026-05-30T14:35:17.668Z", "_jobs": [ { "job": 78640611252, "time": 135, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307480441" }, { "job": 78640611270, "time": 244, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307489340" }, { "job": 78640611268, "time": 287, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307492680" }, { "job": 78640611256, "time": 114, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308906015" }, { "job": 78640611249, "time": 150, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308909563" }, { "job": 78639914336, "time": 226, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307289191" }, { "job": 78640611257, "time": 115, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307478471" }, { "job": 78640611265, "time": 545, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307513574" }, { "job": 78640611276, "time": 507, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307511194" }, { "job": 78640611271, "time": 219, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307487884" } ], "_bioccheck": { "error": 2, "warning": 1, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676982433", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/splineTimeR", "_commit": { "id": "69a96090b8963ba8aad4c6722f3a6615365e0a3e", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380142 }, "_maintainer": { "name": "Herbert Braselmann", "email": "martin.selmansberger@helmholtz-muenchen.de", "login": "hbrmuc", "description": "privat", "uuid": 54470535 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "igraph", "role": "Depends" }, { "package": "limma", "role": "Depends" }, { "package": "GSEABase", "role": "Depends" }, { "package": "gtools", "role": "Depends" }, { "package": "splines", "role": "Depends" }, { "package": "GeneNet", "version": ">= 1.2.13", "role": "Depends" }, { "package": "longitudinal", "version": ">= 1.1.12", "role": "Depends" }, { "package": "FIs", "role": "Depends" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.41.0", "bioc": "3.24" }, { "branch": "release", "version": "1.40.0", "bioc": "3.23" } ], "_topics": [ "geneexpression", "differentialexpression", "timecourse", "regression", "genesetenrichment", "networkenrichment", "networkinference", "graphandnetwork" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 419, "source": "https://www.bioconductor.org/packages/stats/bioc/splineTimeR" }, "_mentions": 3, "_searchresults": 22, "_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/splineTimeR.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "networkProperties", "pathEnrich", "splineDiffExprs", "splineNetRecon", "splinePlot" ], "_datasets": [ { "name": "TCsimData", "title": "Simulated time-course gene expression data set", "object": "TCsimData", "file": "TCsimData.rda", "class": [ "ExpressionSet" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "networkProperties", "title": "Scale-free properties of a network", "topics": [ "networkProperties" ] }, { "page": "pathEnrich", "title": "Pathway enrichment analysis", "topics": [ "pathEnrich" ] }, { "page": "splineDiffExprs", "title": "Differential expression analysis based on natural cubic spline regression models for time-course data", "topics": [ "splineDiffExprs" ] }, { "page": "splineNetRecon", "title": "Network reconstruction based on partial correlation method with shrinkage approach", "topics": [ "splineNetRecon" ] }, { "page": "splinePlot", "title": "Plot spline regression curves of time-course data", "topics": [ "splinePlot" ] }, { "page": "TCsimData", "title": "Simulated time-course gene expression data set", "topics": [ "TCsimData" ] } ], "_rundeps": [ "annotate", "AnnotationDbi", "askpass", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "corpcor", "cpp11", "crayon", "curl", "DBI", "fastmap", "fdrtool", "FIs", "GeneNet", "generics", "glue", "graph", "GSEABase", "gtools", "httr", "igraph", "IRanges", "jsonlite", "KEGGREST", "lattice", "lifecycle", "limma", "longitudinal", "magrittr", "Matrix", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "statmod", "sys", "vctrs", "XML", "xtable", "XVector" ], "_vignettes": [ { "source": "splineTimeR.Rnw", "filename": "splineTimeR.pdf", "title": "splineTimeR", "engine": "utils::Sweave", "headings": [], "created": "2016-03-25 10:26:52", "modified": "2016-10-05 12:59:00", "commits": 6 } ], "_score": 4.12057393120585, "_indexed": true, "_nocasepkg": "splinetimer", "_universes": [ "bioc", "hbrmuc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.41.0", "date": "2026-05-30T10:21:32.000Z", "distro": "noble", "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e", "fileid": "c7649dae89496879f0ddc5c884e46fb68a252c4cd4d4ec3e6c969d07dcb29ff8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676982433" }, { "r": "4.6.0", "os": "linux", "version": "1.41.0", "date": "2026-05-30T10:22:17.000Z", "distro": "noble", "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e", "fileid": "9ba0687893c95f53c8268cdc2286a6ce17f4fabf1e713c84ecc135340cf4100d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676982433" }, { "r": "4.5.3", "os": "mac", "version": "1.41.0", "date": "2026-05-30T14:33:32.000Z", "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e", "fileid": "8d5c1ac74bdbf4f76377f9c3766d08f8201d421c23d7f20320242e4577dc2622", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676982433" }, { "r": "4.6.0", "os": "mac", "version": "1.41.0", "date": "2026-05-30T14:33:47.000Z", "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e", "fileid": "a636a250768ba9a1f7b6ffd5d3603293e8177cba71a9de81fc024fb729528be3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676982433" }, { "r": "4.6.0", "os": "wasm", "version": "1.41.0", "date": "2026-05-30T10:21:10.000Z", "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e", "fileid": "03932657f8c96045a94e91d65a939f7236f014976c48994142715903e466219f", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676982433" }, { "r": "4.7.0", "os": "win", "version": "1.41.0", "date": "2026-05-30T10:25:51.000Z", "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e", "fileid": "1e2dc13b4214e5d2715d30b7670a23df9b417f633b854b280db5bdbb0ca5bf3d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676982433" }, { "r": "4.5.3", "os": "win", "version": "1.41.0", "date": "2026-05-30T10:25:42.000Z", "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e", "fileid": "86d43158b57e262598fc5ac87bf47a0cdcf73dd58073ed20004ad33c6853312b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676982433" }, { "r": "4.6.0", "os": "win", "version": "1.41.0", "date": "2026-05-30T10:20:33.000Z", "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e", "fileid": "5f5297c723ce4cee6f811c411ad3c1875fe158ed55f0e203d6811194bd272f4a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676982433" } ] }