{ "_id": "6abe4f3d99f7aa8c6aa55325", "Package": "SPIA", "Version": "2.65.0", "Date": "2025-1-20", "Title": "Signaling Pathway Impact Analysis (SPIA) using combined evidence\nof pathway over-representation and unusual signaling\nperturbations", "Author": "Adi Laurentiu Tarca , Purvesh Kathri\n and Sorin Draghici ", "Maintainer": "Adi Laurentiu Tarca ", "Description": "This package implements the Signaling Pathway Impact\nAnalysis (SPIA) which uses the information form a list of\ndifferentially expressed genes and their log fold changes\ntogether with signaling pathways topology, in order to identify\nthe pathways most relevant to the condition under the study.", "License": "file LICENSE", "License_restricts_use": "yes", "URL": "http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1", "Collate": "spia.R plotP.R combfunc.R getP2.R makeSPIAdata.R", "LazyLoad": "yes", "Packaged": { "Date": "2026-10-01 11:57:23 UTC", "User": "root" }, "biocViews": "Microarray, GraphAndNetwork", "Config/pak/sysreqs": "make libxml2-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:33:42 UTC", "RemoteUrl": "https://github.com/bioc/SPIA", "RemoteRef": "HEAD", "RemoteSha": "8b360b25028436f7726511462a9d82b6bc9b7b42", "NeedsCompilation": "no", "_user": "bioc", "_type": "src", "_file": "SPIA_2.65.0.tar.gz", "_fileid": "https://r2.ropensci.org/e01fb8ba2e25169d248bae87cb69ae44481abb804f1e64e8e686a657e20035b3", "_filesize": 2692775, "_sha256": "e01fb8ba2e25169d248bae87cb69ae44481abb804f1e64e8e686a657e20035b3", "_expires": "2027-01-09T12:16:58.000Z", "_created": "2026-10-01T11:57:23.000Z", "_published": "2026-10-01T12:17:01.584Z", "_bioccheck": { "error": 1, "warning": 5, "note": 15 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/36858075213", "_status": "success", "_upstream": "https://github.com/bioc/SPIA", "_commit": { "id": "8b360b25028436f7726511462a9d82b6bc9b7b42", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379622 }, "_maintainer": { "name": "Adi Laurentiu Tarca", "email": "atarca@med.wayne.edu" }, "_distro": "resolute", "_jobs": [ { "job": 110357151600, "time": 178, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11160012457" }, { "job": 110357151495, "time": 297, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11160392587" }, { "job": 110357151480, "time": 326, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11161315166" }, { "job": 110357151568, "time": 395, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11161517338" }, { "job": 110357151731, "time": 272, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11161636973" }, { "job": 110355394205, "time": 302, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11160191814" }, { "job": 110357151513, "time": 147, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11160511927" }, { "job": 110357151481, "time": 787, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11161186636" }, { "job": 110357151545, "time": 623, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11160991959" }, { "job": 110357151432, "time": 697, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11161880994" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.14.0", "role": "Depends" }, { "package": "graphics", "role": "Depends" }, { "package": "KEGGgraph", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "graph", "role": "Suggests" }, { "package": "Rgraphviz", "role": "Suggests" }, { "package": "hgu133plus2.db", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 4, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.65.0", "bioc": "3.24" }, { "branch": "release", "version": "2.64.0", "bioc": "3.23" } ], "_topics": [ "microarray", "graphandnetwork" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 471, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 2336, "source": "https://www.bioconductor.org/packages/stats/bioc/SPIA" }, "_mentions": 155, "_searchresults": 138, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/SPIA.html", "LICENSE" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "combfunc", "makeSPIAdata", "plotP", "spia" ], "_datasets": [ { "name": "ALL_Colorectal", "title": "Results from a microarray experiment comparing colorectal cancer samples and normal tissue samples.", "object": "colorectalcancer", "file": "colorectalcancer.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "ALL_Vessels", "title": "Results from a microarray expriment comparing umbilical veins and arteries tissues", "object": "Vessels", "file": "Vessels.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "DE_Colorectal", "title": "Results from a microarray experiment comparing colorectal cancer samples and normal tissue samples.", "object": "colorectalcancer", "file": "colorectalcancer.RData", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "DE_Vessels", "title": "Results from a microarray expriment comparing umbilical veins and arteries tissues", "object": "Vessels", "file": "Vessels.RData", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "top", "title": "Results from a microarray experiment comparing colorectal cancer samples and normal tissue samples.", "object": "colorectalcancer", "file": "colorectalcancer.RData", "class": [ "data.frame" ], "fields": [ "ID", "logFC", "AveExpr", "t", "P.Value", "adj.P.Val", "B", "ENTREZ" ], "rows": 18045, "table": true, "tojson": true } ], "_help": [ { "page": "colorectalcancer", "title": "Results from a microarray experiment comparing colorectal cancer samples and normal tissue samples.", "topics": [ "ALL_Colorectal", "colorectalcancer", "DE_Colorectal", "top" ] }, { "page": "combfunc", "title": "Combining two p-values using Fisher's product or normal inversion method", "topics": [ "combfunc" ] }, { "page": "makeSPIAdata", "title": "Process KGML files for spia analysis", "topics": [ "makeSPIAdata" ] }, { "page": "plotP", "title": "SPIA two-way evidence plot", "topics": [ "plotP" ] }, { "page": "spia", "title": "Signaling Pathway Impact Analysis (SPIA) based on over-representation and signaling perturbations accumulation", "topics": [ "spia" ] }, { "page": "Vessels", "title": "Results from a microarray expriment comparing umbilical veins and arteries tissues", "topics": [ "ALL_Vessels", "DE_Vessels", "Vessels" ] } ], "_rundeps": [ "BiocGenerics", "bitops", "generics", "graph", "KEGGgraph", "RCurl", "Rgraphviz", "XML" ], "_vignettes": [ { "source": "SPIA.Rnw", "filename": "SPIA.pdf", "title": "SPIA", "engine": "utils::Sweave", "headings": [ "Overview", "Pathway analysis with SPIA package", "Parsing up-to-date KEGG xml files for use with SPIA", "Changes in SPIA 2.10 vs 2.9" ], "created": "2013-11-01 20:07:11", "modified": "2013-11-01 20:07:11", "commits": 1 } ], "_score": 6.888563166553205, "_indexed": true, "_nocasepkg": "spia", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.65.0", "date": "2026-10-01T12:00:56.000Z", "distro": "resolute", "commit": "8b360b25028436f7726511462a9d82b6bc9b7b42", "fileid": "https://r2.ropensci.org/5c67e3ff2493a1a56335236ddbc8c57e2f436ef300642b61a8a29b212babc39c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36858075213" }, { "r": "4.6.1", "os": "linux", "version": "2.65.0", "date": "2026-10-01T12:01:26.000Z", "distro": "resolute", "commit": "8b360b25028436f7726511462a9d82b6bc9b7b42", "fileid": "https://r2.ropensci.org/3787afd24f64cff0fcdacdd1821911880d2f36bd894fcab291994caf76dcec63", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36858075213" }, { "r": "4.5.3", "os": "mac", "version": "2.65.0", "date": "2026-10-01T12:12:10.000Z", "commit": "8b360b25028436f7726511462a9d82b6bc9b7b42", "fileid": "https://r2.ropensci.org/2daaa9ecddd77a163eb60ce5f6d73f24126a09e62be53d3ec403f451951a9741", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36858075213" }, { "r": "4.6.1", "os": "mac", "version": "2.65.0", "date": "2026-10-01T12:11:30.000Z", "commit": "8b360b25028436f7726511462a9d82b6bc9b7b42", "fileid": "https://r2.ropensci.org/754d85e5311e0b59d1184542fee143fe1feb569823467a781df4f00ce4a7866d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36858075213" }, { "r": "4.6.0", "os": "wasm", "version": "2.65.0", "date": "2026-10-01T12:00:09.000Z", "commit": "8b360b25028436f7726511462a9d82b6bc9b7b42", "fileid": "https://r2.ropensci.org/1db2d650254fa4c14614e60b560137e631c7fed04840d6c838af82a43c7bc0a2", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36858075213" }, { "r": "4.7.0", "os": "win", "version": "2.65.0", "date": "2026-10-01T12:07:17.000Z", "commit": "8b360b25028436f7726511462a9d82b6bc9b7b42", "fileid": "https://r2.ropensci.org/467675ec8733bd57c419f52b5276e8fe94e64ab75fcd9a3bc469e5922f2e8f9a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36858075213" }, { "r": "4.5.3", "os": "win", "version": "2.65.0", "date": "2026-10-01T12:04:47.000Z", "commit": "8b360b25028436f7726511462a9d82b6bc9b7b42", "fileid": "https://r2.ropensci.org/89450b69f0d84bf9c3e30958a097c8e10c2eec3230d8fdfc985588b1ea06b699", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36858075213" }, { "r": "4.6.1", "os": "win", "version": "2.65.0", "date": "2026-10-01T12:05:20.000Z", "commit": "8b360b25028436f7726511462a9d82b6bc9b7b42", "fileid": "https://r2.ropensci.org/dc63ff8c1d65a3ed02942369f738cb890be3ebf625976142b8c2df3bcca3a976", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36858075213" } ] }