{ "_id": "6a1b00fc1d7bb097a09ffd44", "Package": "SBGNview", "Title": "\"SBGNview: Data Analysis, Integration and Visualization on SBGN\nPathways\"", "Description": "SBGNview is a tool set for pathway based data\nvisalization, integration and analysis. SBGNview is similar and\ncomplementary to the widely used Pathview, with the following\nkey features: 1. Pathway definition by the widely adopted\nSystems Biology Graphical Notation (SBGN); 2. Supports multiple\nmajor pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB,\nPANTHER, METACROP) and user defined pathways; 3. Covers 5,200\nreference pathways and over 3,000 species by default; 4.\nExtensive graphics controls, including glyph and edge\nattributes, graph layout and sub-pathway highlight; 5. SBGN\npathway data manipulation, processing, extraction and analysis.", "Version": "1.27.0", "Author": "Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo", "Maintainer": "Weijun Luo ", "RdMacros": "Rdpack", "License": "AGPL-3", "LazyData": "FALSE", "Collate": "SBGN.to.SVG.R SBGNview.R SBGNview.obj.fun.R color.panel.R\ndata.R download.utilities.R highlight.utilities.R\nmapping.utilities.R parsing.utilities.R plot.utilities.R zzz.R", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "biocViews": "GeneTarget, Pathways, GraphAndNetwork, Visualization,\nGeneSetEnrichment, DifferentialExpression, GeneExpression,\nMicroarray, RNASeq, Genetics, Metabolomics, Proteomics,\nSystemsBiology, Sequencing, GeneTarget", "URL": "https://github.com/datapplab/SBGNview", "BugReports": "https://github.com/datapplab/SBGNview/issues", "Config/pak/sysreqs": "cmake libglpk-dev make libpng-dev librsvg2-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:50:27 UTC", "RemoteUrl": "https://github.com/bioc/SBGNview", "RemoteRef": "HEAD", "RemoteSha": "afcc5fe340575a69d7e0f909ef03c1045dc20442", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:54:34 UTC", "User": "root" }, "MD5sum": "8d4cdead123d60b5e716c91e24868530", "_user": "bioc", "_type": "src", "_file": "SBGNview_1.27.0.tar.gz", "_fileid": "946ede2f22a9252c087794c9990d2edbe778a43aaf25b191df981deb60b91e2d", "_filesize": 1083937, "_sha256": "946ede2f22a9252c087794c9990d2edbe778a43aaf25b191df981deb60b91e2d", "_created": "2026-05-30T09:54:34.000Z", "_published": "2026-05-30T15:23:40.138Z", "_jobs": [ { "job": 78641010220, "time": 233, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307592684" }, { "job": 78641010232, "time": 424, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307611368" }, { "job": 78641010228, "time": 439, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307612762" }, { "job": 78641010226, "time": 241, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7309207679" }, { "job": 78641010245, "time": 307, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7309215853" }, { "job": 78640036092, "time": 337, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307336086" }, { "job": 78641010216, "time": 165, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307585314" }, { "job": 78641010257, "time": 672, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307635729" }, { "job": 78641010254, "time": 667, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307635295" }, { "job": 78641010246, "time": 323, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307602460" } ], "_bioccheck": { "error": 3, "warning": 1, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677215155", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/SBGNview", "_commit": { "id": "afcc5fe340575a69d7e0f909ef03c1045dc20442", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380627 }, "_maintainer": { "name": "Weijun Luo", "email": "luo_weijun@yahoo.com", "login": "wluo1", "description": "", "uuid": 36652110 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "pathview", "role": "Depends" }, { "package": "SBGNview.data", "role": "Depends" }, { "package": "Rdpack", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "xml2", "role": "Imports" }, { "package": "rsvg", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "rmarkdown", "role": "Imports" }, { "package": "knitr", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "KEGGREST", "role": "Imports" }, { "package": "bookdown", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "gage", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.27.0", "bioc": "3.24" }, { "branch": "release", "version": "1.26.0", "bioc": "3.23" } ], "_topics": [ "genetarget", "pathways", "graphandnetwork", "visualization", "genesetenrichment", "differentialexpression", "geneexpression", "microarray", "rnaseq", "genetics", "metabolomics", "proteomics", "systemsbiology", "sequencing" ], "_stars": 29, "_contributors": [ { "user": "kovidhv", "count": 115, "uuid": 20483951 }, { "user": "wluo1", "count": 17, "uuid": 36652110 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 526, "source": "https://www.bioconductor.org/packages/stats/bioc/SBGNview" }, "_devurl": "https://github.com/datapplab/sbgnview", "_searchresults": 28, "_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/readme.html", "extra/readme.md", "extra/SBGNview.html", "manual.pdf" ], "_homeurl": "https://github.com/datapplab/sbgnview", "_realowner": "bioc", "_cranurl": false, "_exports": [ "changeDataId", "changeIds", "downloadSbgnFile", "findPathways", "highlightArcs", "highlightNodes", "highlightPath", "loadMappingTable", "outputFile", "outputFile<-", "renderSbgn", "sbgn.gsets", "sbgnNodes", "SBGNview" ], "_datasets": [ { "name": "mapped.ids", "title": "IDs mappable by SBGNview", "object": "mapped.ids", "file": "mapped.ids.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "pathways.info", "title": "Information of collected pathways", "object": "pathways.info", "file": "pathways.info.RData", "class": [ "data.frame" ], "fields": [ "file.name", "database", "uri", "sub.database", "pathway.id", "pathway.name", "macromolecule.ID.type", "simple.chemical.ID.type" ], "rows": 5200, "table": true, "tojson": true }, { "name": "pathways.stats", "title": "Number of pathways collected", "object": "pathways.stats", "file": "pathways.stats.RData", "class": [ "data.frame" ], "fields": [ "database", "sub.database", "Freq" ], "rows": 5, "table": true, "tojson": true }, { "name": "SBGNhub.id.mapping.tables", "title": "Mapping tables available in SBGNhub", "object": "SBGNhub.id.mapping.tables", "file": "SBGNhub.id.mapping.tables.RData", "class": [ "matrix", "array" ], "fields": [ "SBGNhub.id.mapping.tables" ], "rows": 822, "table": true, "tojson": true } ], "_help": [ { "page": "plus-.SBGNview", "title": "Generic function to modify SBGN graph features", "topics": [ "+.SBGNview" ] }, { "page": "arc-class", "title": "An object to store arc information", "topics": [ "arc-class" ] }, { "page": "changeDataId", "title": "Change the data IDs of input omics data matrix", "topics": [ "changeDataId" ] }, { "page": "changeIds", "title": "Change vector of input IDs to another ID type", "topics": [ "changeIds" ] }, { "page": "downloadSbgnFile", "title": "Download pre-generated SBGN-ML file from GitHub", "topics": [ "downloadSbgnFile" ] }, { "page": "findPathways", "title": "Retrieve pathways by keywords", "topics": [ "findPathways" ] }, { "page": "glyph-class", "title": "An object to store glyph information", "topics": [ "glyph-class" ] }, { "page": "highlightArcs", "title": "Highlight arcs by arc class", "topics": [ "highlightArcs" ] }, { "page": "highlightNodes", "title": "Highlight input nodes", "topics": [ "highlightNodes" ] }, { "page": "highlightPath", "title": "Highlight shortest path between two nodes", "topics": [ "highlightPath" ] }, { "page": "loadMappingTable", "title": "Generate ID mapping table from input and output ID types", "topics": [ "loadMappingTable" ] }, { "page": "mapped.ids", "title": "IDs mappable by SBGNview", "topics": [ "mapped.ids" ] }, { "page": "outputFile", "title": "Retrieve output file information from a SBGNview object", "topics": [ "outputFile" ] }, { "page": "outputFile-set", "title": "Set or change output file information for a SBGNview object", "topics": [ "outputFile<-" ] }, { "page": "pathways.info", "title": "Information of collected pathways", "topics": [ "pathways.info" ] }, { "page": "pathways.stats", "title": "Number of pathways collected", "topics": [ "pathways.stats" ] }, { "page": "print.SBGNview", "title": "Generate image files", "topics": [ "print.SBGNview" ] }, { "page": "renderSbgn", "title": "Overlay omics data on a SBGN pathway graph and output image files.", "topics": [ "renderSbgn" ] }, { "page": "sbgn.gsets", "title": "Retrieve gene list or compound list from collected databases", "topics": [ "sbgn.gsets" ] }, { "page": "SBGNhub.id.mapping.tables", "title": "Mapping tables available in SBGNhub", "topics": [ "SBGNhub.id.mapping.tables" ] }, { "page": "sbgnNodes", "title": "Extract glyph information", "topics": [ "sbgnNodes" ] }, { "page": "SBGNview", "title": "Overlay omics data on SBGN pathway diagram and output image files.", "topics": [ "SBGNview" ] }, { "page": "spline.arc-class", "title": "An object to store information of spline arcs", "topics": [ "spline.arc-class" ] } ], "_readme": "https://github.com/bioc/SBGNview/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "base64enc", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "bitops", "blob", "bookdown", "bslib", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "digest", "evaluate", "fastmap", "fontawesome", "fs", "generics", "GenomicRanges", "glue", "graph", "highr", "htmltools", "httr", "igraph", "IRanges", "jquerylib", "jsonlite", "KEGGgraph", "KEGGREST", "knitr", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "org.Hs.eg.db", "pathview", "pkgconfig", "png", "R6", "rappdirs", "rbibutils", "RCurl", "Rdpack", "Rgraphviz", "rlang", "rmarkdown", "RSQLite", "rsvg", "S4Arrays", "S4Vectors", "sass", "SBGNview.data", "Seqinfo", "SparseArray", "SummarizedExperiment", "sys", "tinytex", "vctrs", "xfun", "XML", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "pathway.enrichment.analysis.Rmd", "filename": "pathway.enrichment.analysis.html", "title": "SBGNview Based Pathway Analysis and Visualization Workflow", "author": "Xiaoxi Dong, Kovidh Vegesna, kvegesna (AT) uncc.edu, Weijun Luo, luo_weijun (AT) yahoo.com", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Citation", "Installation and quick start", "Complete pathway analysis + visualization workflow", "Load the gene (RNA-seq) data", "Gene sets from SBGNview pathway collection", "Load gene set for mouse with ENSEMBL gene IDs", "Pathway or gene set analysis using GAGE", "Visualize perturbations in top SBGN pathways", "Calculate fold changes or gene perturbations", "Visualize pathway perturbations by SBNGview", "SBGNview with SummarizedExperiment object", "Session Info" ], "created": "2019-05-28 18:20:45", "modified": "2021-03-03 02:15:32", "commits": 4 }, { "source": "SBGNview.quick.start.Rmd", "filename": "SBGNview.quick.start.html", "title": "SBGNview Quick Start", "author": "Kovidh Vegesna, kvegesna (AT) uncc.edu, Weijun Luo, luo_weijun (AT) yahoo.com", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Citation", "Installation", "Prerequisites", "Install SBGNview", "Quick example", "Additional information", "Session Info" ], "created": "2021-02-25 23:03:41", "modified": "2021-02-27 19:59:26", "commits": 2 }, { "source": "SBGNview.Vignette.Rmd", "filename": "SBGNview.Vignette.html", "title": "SBGNview: Data Analysis, Integration and Visualization on Massive SBGN Pathway Collections", "author": "Xiaoxi Dong, Kovidh Vegesna, kvegesna (AT) uncc.edu, Weijun Luo, luo_weijun (AT) yahoo.com", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Citation", "Installation and quick start", "Getting started", "Load the SBGNview package, together with pathview and other dependencies", "Accessing help and documentation", "SBGN pathway file (SBGN-ML)", "Two tiers of support and two scenarios with SBGN based pathways", "Load SBGNview's SBGN-ML pathway data collection", "Information about the SBGN-ML pathway data collection", "Search for pathways by keywords", "Different layout for the same pathway", "Custom SBGN-ML files", "Basic visualization", "Visualize gene data", "Visualize compound data", "Visualize both gene data and compound data", "Work with SBGNview object", "Structure of SBGNview object", "Extract glyphs and arcs infromation from SBGNview object", "Modify SBGNview object directly", "Change output file name and format of SBGNview objects", "Updating & modifying graphs", "Hightlight nodes", "Highlight all nodes", "Highlight nodes by class", "Show node IDs instead of node labels", "Adjust node labels.", "Label position, font size, color, change labels", "Label text wrapping into multiple lines", "When one input ID maps to multiple nodes", "Highlight arcs and paths", "Different layouts for the same pathway", "SVG Editing Tool", "ID mapping", "Map between two types of IDs", "Extract molecule list from pathways", "Example using selected database", "Use Reactome pathway database", "Test SBGN reference cards", "FAQs", "Color key", "Turn off color key", "Session Info", "References" ], "created": "2019-05-28 18:20:45", "modified": "2021-02-25 23:03:41", "commits": 4 } ], "_score": 6.386677283960838, "_indexed": true, "_nocasepkg": "sbgnview", "_universes": [ "bioc", "wluo1", "datapplab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.27.0", "date": "2026-05-30T10:41:45.000Z", "distro": "noble", "commit": "afcc5fe340575a69d7e0f909ef03c1045dc20442", "fileid": "bc402314fc30dd0b0cf762ad5da226e1cee58c536ab23227a6c4f62e39fce9ab", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677215155" }, { "r": "4.6.0", "os": "linux", "version": "1.27.0", "date": "2026-05-30T10:41:50.000Z", "distro": "noble", "commit": "afcc5fe340575a69d7e0f909ef03c1045dc20442", "fileid": "4277c12f4d1f987cb1110dec19b963b26b50da6e5790022bc9c6d61582e37677", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677215155" }, { "r": "4.5.3", "os": "mac", "version": "1.27.0", "date": "2026-05-30T15:19:47.000Z", "commit": "afcc5fe340575a69d7e0f909ef03c1045dc20442", "fileid": "01be80351a961ac152326d2d7c72272dcd31b232fd05510ef129bd29ee960d4e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677215155" }, { "r": "4.6.0", "os": "mac", "version": "1.27.0", "date": "2026-05-30T15:20:03.000Z", "commit": "afcc5fe340575a69d7e0f909ef03c1045dc20442", "fileid": "a63909078d4215bf048946ec01104fcc68c43cd2588e37599fe7c34936e20fc7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677215155" }, { "r": "4.6.0", "os": "wasm", "version": "1.27.0", "date": "2026-05-30T10:41:02.000Z", "commit": "afcc5fe340575a69d7e0f909ef03c1045dc20442", "fileid": "750cd8642dc73b3521cc8a66d2c2fc12b62af45bfe1528dabe7aa939ada0600b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677215155" }, { "r": "4.7.0", "os": "win", "version": "1.27.0", "date": "2026-05-30T10:45:36.000Z", "commit": "afcc5fe340575a69d7e0f909ef03c1045dc20442", "fileid": "7d3f8f6b24978a093975f6ff47628cd2279209b48728fe3ff0b1b21b796d89ff", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677215155" }, { "r": "4.5.3", "os": "win", "version": "1.27.0", "date": "2026-05-30T10:45:40.000Z", "commit": "afcc5fe340575a69d7e0f909ef03c1045dc20442", "fileid": "ad15adc54e40ccbbc4700c9d091e8147343720b67f7c9aac1f3a5ac9ae2b98a6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677215155" }, { "r": "4.6.0", "os": "win", "version": "1.27.0", "date": "2026-05-30T10:40:03.000Z", "commit": "afcc5fe340575a69d7e0f909ef03c1045dc20442", "fileid": "be55b063e1ca105e5484a78f0e18d7d780edcb3b86dedac9fea663c52ee4813a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677215155" } ] }