{ "_id": "6a1aec0d1d7bb097a09f4051", "Package": "ROntoTools", "Type": "Package", "Title": "R Onto-Tools suite", "Version": "2.40.0", "Author": "Calin Voichita and Sahar Ansari\n and Sorin Draghici\n", "Maintainer": "Sorin Draghici ", "Description": "Suite of tools for functional analysis.", "biocViews": "NetworkAnalysis, Microarray, GraphsAndNetworks", "License": "CC BY-NC-ND 4.0 + file LICENSE", "RoxygenNote": "5.0.1", "Config/pak/sysreqs": "make libpng-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:37:32 UTC", "RemoteUrl": "https://github.com/bioc/ROntoTools", "RemoteRef": "RELEASE_3_23", "RemoteSha": "203d61bba13b1022e204010014213ea6c2409986", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:42:27 UTC", "User": "root" }, "MD5sum": "42840f4c404cce5c8f6df1bf326554e5", "_user": "bioc-release", "_type": "src", "_file": "ROntoTools_2.40.0.tar.gz", "_fileid": "3665305e8b904b66016f029cb094949ef77941a822615413a32b65fa30f904d3", "_filesize": 1563771, "_sha256": "3665305e8b904b66016f029cb094949ef77941a822615413a32b65fa30f904d3", "_created": "2026-05-30T09:42:27.000Z", "_published": "2026-05-30T13:54:21.517Z", "_jobs": [ { "job": 78640382246, "time": 154, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307407301" }, { "job": 78640382253, "time": 231, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307414109" }, { "job": 78640382252, "time": 237, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7307414835" }, { "job": 78640382264, "time": 162, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7308665365" }, { "job": 78640382265, "time": 158, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7308666080" }, { "job": 78639786857, "time": 201, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307261420" }, { "job": 78640382248, "time": 108, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307403146" }, { "job": 78640382267, "time": 175, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7307412163" }, { "job": 78640382266, "time": 167, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7307411361" }, { "job": 78640382262, "time": 177, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7307412191" } ], "_bioccheck": { "error": 2, "warning": 7, "note": 16 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680156174", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/ROntoTools", "_commit": { "id": "203d61bba13b1022e204010014213ea6c2409986", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379852 }, "_maintainer": { "name": "Sorin Draghici", "email": "sorin@advaitabio.com", "login": "sdraghi", "description": "", "uuid": 60202389 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "methods", "role": "Depends" }, { "package": "graph", "role": "Depends" }, { "package": "boot", "role": "Depends" }, { "package": "KEGGREST", "role": "Depends" }, { "package": "KEGGgraph", "role": "Depends" }, { "package": "Rgraphviz", "role": "Depends" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 2, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.41.0", "bioc": "3.24" }, { "branch": "release", "version": "2.40.0", "bioc": "3.23" } ], "_topics": [ "networkanalysis", "microarray", "graphsandnetworks" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 571, "source": "https://www.bioconductor.org/packages/stats/bioc/ROntoTools" }, "_mentions": 7, "_searchresults": 24, "_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/ROntoTools.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "alpha1MR", "alphaMLG", "compute.fisher", "compute.normalInv", "keggPathwayGraphs", "keggPathwayNames", "nodeWeights", "pDis", "pe", "peEdgeRenderInfo", "peNodeRenderInfo", "plot", "setEdgeWeights", "setNodeWeights", "Summary" ], "_help": [ { "page": "alpha1MR", "title": "Compute alpha weights", "topics": [ "alpha1MR" ] }, { "page": "alphaMLG", "title": "Compute alpha weights", "topics": [ "alphaMLG" ] }, { "page": "compute.fisher", "title": "Combine independent p-values using the Fisher method", "topics": [ "compute.fisher" ] }, { "page": "compute.normalInv", "title": "Combine independent p-values using the normal inversion method", "topics": [ "compute.normalInv" ] }, { "page": "keggPathwayGraphs", "title": "Download and parse KEGG pathway data", "topics": [ "keggPathwayGraphs" ] }, { "page": "keggPathwayNames", "title": "Obtain KEGG pathway titles", "topics": [ "keggPathwayNames" ] }, { "page": "nodeWeights", "title": "Retrieve the node weights of a graph", "topics": [ "nodeWeights", "nodeWeights,graph,character-method", "nodeWeights,graph,missing-method", "nodeWeights,graph,numeric-method" ] }, { "page": "pDis", "title": "Primary dis-regulation: Pathway analysis approach based on the unexplained dis-regulation of genes", "topics": [ "pDis" ] }, { "page": "pDisPathway-class", "title": "Class that encodes the result of pDis analysis for a single pathway", "topics": [ "pDisPathway-class" ] }, { "page": "pDisRes-class", "title": "Primary dis-regulation (pDis) result class", "topics": [ "pDisRes-class" ] }, { "page": "pe", "title": "Pathway-Express: Pathway analysis of signaling pathways", "topics": [ "pe" ] }, { "page": "peEdgeRenderInfo", "title": "Extract edge render information from a 'pePathway-class' object", "topics": [ "peEdgeRenderInfo" ] }, { "page": "peNodeRenderInfo", "title": "Extract node render information from a 'pePathway-class' object", "topics": [ "peNodeRenderInfo" ] }, { "page": "pePathway-class", "title": "Class that encodes the result of Pathway-Express for a single pathway", "topics": [ "pePathway-class" ] }, { "page": "peRes-class", "title": "Pathway-Express result class", "topics": [ "peRes-class" ] }, { "page": "plot.pePathway-methods", "title": "Plot pathway level statistics", "topics": [ "plot,pePathway,character-method", "plot,pePathway,missing-method" ] }, { "page": "plot.peRes-methods", "title": "Plot Pathway-Express result", "topics": [ "plot,peRes,character-method", "plot,peRes,missing-method" ] }, { "page": "setEdgeWeights", "title": "Set gene weights based on edge type", "topics": [ "setEdgeWeights" ] }, { "page": "setNodeWeights", "title": "Set node weights", "topics": [ "setNodeWeights" ] }, { "page": "Summary-pDisRes-method", "title": "Summarize the results of a Pathway-Express analysis", "topics": [ "Summary,pDisRes-method" ] }, { "page": "Summary-peRes-method", "title": "Summarize the results of a Pathway-Express analysis", "topics": [ "Summary,peRes-method" ] }, { "page": "summary.pDisRes", "title": "Summarize the results of a primary dis-regulation (pDis) analysis", "topics": [ "summary.pDisRes" ] }, { "page": "summary.peRes", "title": "Summarize the results of a Pathway-Express analysis", "topics": [ "summary.peRes" ] } ], "_rundeps": [ "askpass", "BiocGenerics", "Biostrings", "bitops", "boot", "crayon", "curl", "generics", "graph", "httr", "IRanges", "jsonlite", "KEGGgraph", "KEGGREST", "mime", "openssl", "png", "R6", "RCurl", "Rgraphviz", "S4Vectors", "Seqinfo", "sys", "XML", "XVector" ], "_vignettes": [ { "source": "rontotools.Rnw", "filename": "rontotools.pdf", "title": "ROntoTools", "engine": "utils::Sweave", "headings": [], "created": "2013-03-22 22:40:44", "modified": "2016-04-15 05:40:35", "commits": 3 } ], "_score": 5.304490527773488, "_indexed": false, "_nocasepkg": "rontotools", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/ROntoTools", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.40.0", "date": "2026-05-30T10:07:37.000Z", "distro": "noble", "commit": "203d61bba13b1022e204010014213ea6c2409986", "fileid": "2e0ff64a6e78184fde682a7826e2f404298b1927b3724964193e217151afedc5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680156174" }, { "r": "4.6.0", "os": "linux", "version": "2.40.0", "date": "2026-05-30T10:07:42.000Z", "distro": "noble", "commit": "203d61bba13b1022e204010014213ea6c2409986", "fileid": "7beb89eb339c7dfc25dfa38d62a358efac0bf71f53d6d9ea5346a4fc2689c93a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680156174" }, { "r": "4.5.3", "os": "mac", "version": "2.40.0", "date": "2026-05-30T13:52:44.000Z", "commit": "203d61bba13b1022e204010014213ea6c2409986", "fileid": "9e8b0d30809f781c97eb4c959bc634d069838be11e0499fdaf795b0f1a37d016", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680156174" }, { "r": "4.6.0", "os": "mac", "version": "2.40.0", "date": "2026-05-30T13:52:49.000Z", "commit": "203d61bba13b1022e204010014213ea6c2409986", "fileid": "2e960071cc076e5ec159c23d78c4f8231c93cd338af774b2de12db200d650242", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680156174" }, { "r": "4.6.0", "os": "wasm", "version": "2.40.0", "date": "2026-05-30T10:07:22.000Z", "commit": "203d61bba13b1022e204010014213ea6c2409986", "fileid": "63c3f701941f5e586e656f64ff9fce934cd1c9977ee4244aa4a0b9f1ac2e63b8", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680156174" }, { "r": "4.7.0", "os": "win", "version": "2.40.0", "date": "2026-05-30T10:07:13.000Z", "commit": "203d61bba13b1022e204010014213ea6c2409986", "fileid": "a6ab2fa1120b6427373349fbfb41127aa73449177bf4ffd93c0cb937df5ed703", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680156174" }, { "r": "4.5.3", "os": "win", "version": "2.40.0", "date": "2026-05-30T10:07:09.000Z", "commit": "203d61bba13b1022e204010014213ea6c2409986", "fileid": "a3a1ddc01b9130cfb9383e9dc32c3a061b280a12f944ddab5a7a5cbe1314ae32", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680156174" }, { "r": "4.6.0", "os": "win", "version": "2.40.0", "date": "2026-05-30T10:07:15.000Z", "commit": "203d61bba13b1022e204010014213ea6c2409986", "fileid": "3e72fa7b133bf1b94f03a34583278c2cebc5ca89d9dae395afef69ed7e0cccd6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680156174" } ] }