{ "_id": "6aca20d1fe5cc25786e85018", "Package": "SBGNview.data", "Title": "Supporting datasets for SBGNview package", "Description": "This package contains: 1. A microarray gene expression\ndataset from a human breast cancer study. 2. A RNA-Seq gene\nexpression dataset from a mouse study on IFNG knockout. 3. ID\nmapping tables between gene IDs and SBGN-ML file glyph IDs. 4.\nPercent of orthologs detected in other species of the genes in\na pathway. Cutoffs of this percentage for defining if a pathway\nexists in another species. 5. XML text of SBGN-ML files for all\npre-collected pathways.", "Version": "1.26.0", "Author": "Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo", "Maintainer": "Weijun Luo ", "License": "AGPL-3", "Collate": "data.R", "LazyData": "FALSE", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "biocViews": "ExperimentData, CancerData, BreastCancerData,\nMicroarrayData, GEO, RNASeqData", "Config/pak/sysreqs": "cmake make libuv1-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:33:21 UTC", "RemoteUrl": "https://github.com/bioc/SBGNview.data", "RemoteRef": "RELEASE_3_23", "RemoteSha": "b1663a69ae087b9b61c3f2c8acf464d799eb7f5a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-10 11:12:49 UTC", "User": "root" }, "_user": "bioc-release", "_type": "src", "_file": "SBGNview.data_1.26.0.tar.gz", "_fileid": "https://r2.ropensci.org/e7076f62bff31209e701c1308bf36b1053eebb9dc54c310b7d13ba94d2d5d7f1", "_filesize": 57482284, "_sha256": "e7076f62bff31209e701c1308bf36b1053eebb9dc54c310b7d13ba94d2d5d7f1", "_expires": "2027-01-18T11:26:06.000Z", "_created": "2026-10-10T11:12:49.000Z", "_published": "2026-10-10T11:26:09.572Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047410779", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 1, "warning": 1, "note": 7 }, "_upstream": "https://github.com/bioc/SBGNview.data", "_commit": { "id": "b1663a69ae087b9b61c3f2c8acf464d799eb7f5a", "author": "lshep ", "committer": "lshep ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379601 }, "_maintainer": { "name": "Weijun Luo", "email": "luo_weijun@yahoo.com", "login": "wluo1", "description": "", "uuid": 36652110 }, "_distro": "resolute", "_jobs": [ { "job": 114201745076, "time": 143, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11668332955" }, { "job": 114201745064, "time": 225, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11667918464" }, { "job": 114201745199, "time": 199, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11668372899" }, { "job": 114199664496, "time": 734, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11668117884" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "knitr", "role": "Imports" }, { "package": "rmarkdown", "role": "Imports" }, { "package": "bookdown", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.27.0", "bioc": "3.24", "repository": "data/experiment" }, { "branch": "release", "version": "1.26.0", "bioc": "3.23", "repository": "data/experiment" } ], "_topics": [ "experimentdata", "cancerdata", "breastcancerdata", "microarraydata", "geo", "rnaseqdata", "datapkg" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 3, "_datapkg": true, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/SBGNview.data.html" ], "_cranurl": false, "_exports": [], "_datasets": [ { "name": "cancer.ds", "title": "A demo microarray dataset from a cancer study", "object": "cancer.ds", "file": "cancer.ds.RData", "class": [ "SummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "chebi_compound.name", "title": "Mapping table between two types of IDs", "object": "chebi_compound.name", "file": "chebi_compound.name.RData", "class": [ "data.frame" ], "fields": [ "chebi", "compound.name" ], "rows": 285207, "table": true, "tojson": true }, { "name": "chebi_kegg", "title": "Mapping table between two types of IDs", "object": "chebi_kegg", "file": "chebi_kegg.RData", "class": [ "data.frame" ], "fields": [ "chebi", "kegg" ], "rows": 20692, "table": true, "tojson": true }, { "name": "chebi_metacyc.SBGN", "title": "Mapping table between two types of IDs", "object": "chebi_metacyc.SBGN", "file": "chebi_metacyc.SBGN.RData", "class": [ "matrix", "array" ], "fields": [ "chebi", "metacyc.SBGN" ], "rows": 60659, "table": true, "tojson": true }, { "name": "chebi_pathway.id", "title": "Mapping table between two types of IDs", "object": "chebi_pathway.id", "file": "chebi_pathway.id.RData", "class": [ "data.frame" ], "fields": [ "chebi", "pathway.id" ], "rows": 79911, "table": true, "tojson": true }, { "name": "chebi_pathwayCommons", "title": "Mapping table between two types of IDs", "object": "chebi_pathwayCommons", "file": "chebi_pathwayCommons.RData", "class": [ "matrix", "array" ], "fields": [ "pathwayCommons", "chebi" ], "rows": 60425, "table": true, "tojson": true }, { "name": "compound.name_kegg", "title": "Mapping table between two types of IDs", "object": "compound.name_kegg", "file": "compound.name_kegg.RData", "class": [ "data.frame" ], "fields": [ "kegg", "compound.name" ], "rows": 61143, "table": true, "tojson": true }, { "name": "compound.name_pathway.id", "title": "Mapping table between two types of IDs", "object": "compound.name_pathway.id", "file": "compound.name_pathway.id.RData", "class": [ "data.frame" ], "fields": [ "compound.name", "pathway.id" ], "rows": 571283, "table": true, "tojson": true }, { "name": "compound.name_pathwayCommons", "title": "Mapping table between two types of IDs", "object": "compound.name_pathwayCommons", "file": "compound.name_pathwayCommons.RData", "class": [ "data.frame" ], "fields": [ "compound.name", "pathwayCommons" ], "rows": 298727, "table": true, "tojson": true }, { "name": "ENZYME_pathway.id", "title": "Mapping table between two types of IDs", "object": "ENZYME_pathway.id", "file": "ENZYME_pathway.id.RData", "class": [ "data.frame" ], "fields": [ "ENZYME", "pathway.id" ], "rows": 16601, "table": true, "tojson": true }, { "name": "hsa_ENTREZID_pathwayCommons", "title": "Mapping table between two types of IDs", "object": "hsa_ENTREZID_pathwayCommons", "file": "hsa_ENTREZID_pathwayCommons.RData", "class": [ "matrix", "array" ], "fields": [ "ENTREZID", "pathwayCommons" ], "rows": 384671, "table": true, "tojson": true }, { "name": "hsa_KO_ENTREZID", "title": "Mapping table between two types of IDs", "object": "hsa_KO_ENTREZID", "file": "hsa_KO_ENTREZID.RData", "class": [ "data.frame" ], "fields": [ "KO", "ENTREZID", "species" ], "rows": 10446, "table": true, "tojson": true }, { "name": "hsa_pathwayCommons_ENSEMBL", "title": "Mapping table between two types of IDs", "object": "hsa_pathwayCommons_ENSEMBL", "file": "hsa_pathwayCommons_ENSEMBL.RData", "class": [ "matrix", "array" ], "fields": [ "pathwayCommons", "ENSEMBL" ], "rows": 383983, "table": true, "tojson": true }, { "name": "IFNg", "title": "RNA-Seq result from a mouse IFNG knockout experiment", "object": "IFNg", "file": "IFNg.RData", "class": [ "SummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "kegg_pathwayCommons", "title": "Mapping table between two types of IDs", "object": "kegg_pathwayCommons", "file": "kegg_pathwayCommons.RData", "class": [ "data.frame" ], "fields": [ "kegg", "pathwayCommons" ], "rows": 6448, "table": true, "tojson": true }, { "name": "KO_pathway.id", "title": "Mapping table between two types of IDs", "object": "KO_pathway.id", "file": "KO_pathway.id.RData", "class": [ "data.frame" ], "fields": [ "KO", "pathway.id" ], "rows": 47719, "table": true, "tojson": true }, { "name": "KO_pathwayCommons", "title": "Mapping table between two types of IDs", "object": "KO_pathwayCommons", "file": "KO_pathwayCommons.RData", "class": [ "data.frame" ], "fields": [ "KO", "pathwayCommons" ], "rows": 88148, "table": true, "tojson": true }, { "name": "mmu_KO_ENSEMBL", "title": "Mapping table between two types of IDs", "object": "mmu_KO_ENSEMBL", "file": "mmu_KO_ENSEMBL.RData", "class": [ "matrix", "array" ], "fields": [ "KO", "ENSEMBL" ], "rows": 11016, "table": true, "tojson": true }, { "name": "mmu_KO_ENTREZID", "title": "Mapping table between two types of IDs", "object": "mmu_KO_ENTREZID", "file": "mmu_KO_ENTREZID.RData", "class": [ "data.frame" ], "fields": [ "KO", "ENTREZID", "species" ], "rows": 11105, "table": true, "tojson": true }, { "name": "mmu_pathwayCommons_ENSEMBL", "title": "Mapping table between two types of IDs", "object": "mmu_pathwayCommons_ENSEMBL", "file": "mmu_pathwayCommons_ENSEMBL.RData", "class": [ "matrix", "array" ], "fields": [ "ENSEMBL", "pathwayCommons" ], "rows": 619656, "table": true, "tojson": true }, { "name": "mmu_pathwayCommons_ENTREZID", "title": "Mapping table between two types of IDs", "object": "mmu_pathwayCommons_ENTREZID", "file": "mmu_pathwayCommons_ENTREZID.RData", "class": [ "matrix", "array" ], "fields": [ "pathwayCommons", "ENTREZID" ], "rows": 628413, "table": true, "tojson": true }, { "name": "pathway.completeness.cutoff.info", "title": "Cutoffs of pathway completeness used for defining existance of pathway in a species", "object": "pathway.completeness.cutoff.info", "file": "pathway.completeness.cutoff.info.RData", "class": [ "data.frame" ], "fields": [ "pathway", "cutoff", "ANOVA.F.stat", "ANOVA.P" ], "rows": 3529, "table": true, "tojson": true }, { "name": "pathway.species.pct_Mapped", "title": "Pathway completeness in a species", "object": "pathway.species.pct_Mapped", "file": "pathway.species.pct_Mapped.RData", "class": [ "data.frame" ], "fields": [ "pathway", "species", "ref.pathway.protein.count", "pct.mapped.species.pathway", "species.pathway.protein.count" ], "rows": 6939443, "table": true, "tojson": false }, { "name": "pathwayCommons_SYMBOL", "title": "Mapping table between two types of IDs", "object": "pathwayCommons_SYMBOL", "file": "pathwayCommons_SYMBOL.RData", "class": [ "data.frame" ], "fields": [ "SYMBOL", "pathwayCommons", "species" ], "rows": 406940, "table": true, "tojson": true }, { "name": "sbgn.xmls", "title": "XML code of a SBGN-ML file", "object": "sbgn.xmls", "file": "sbgn.xmls.RData", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "SYMBOL_pathway.id", "title": "Mapping table between two types of IDs", "object": "SYMBOL_pathway.id", "file": "SYMBOL_pathway.id.RData", "class": [ "data.frame" ], "fields": [ "SYMBOL", "pathway.id" ], "rows": 252730, "table": true, "tojson": true } ], "_help": [ { "page": "cancer.ds", "title": "A demo microarray dataset from a cancer study", "topics": [ "cancer.ds" ] }, { "page": "IFNg", "title": "RNA-Seq result from a mouse IFNG knockout experiment", "topics": [ "IFNg" ] }, { "page": "mapping", "title": "Mapping table between two types of IDs", "topics": [ "chebi_compound.name", "chebi_kegg", "chebi_metacyc.SBGN", "chebi_pathway.id", "chebi_pathwayCommons", "compound.name_kegg", "compound.name_pathway.id", "compound.name_pathwayCommons", "ENZYME_pathway.id", "hsa_ENTREZID_pathwayCommons", "hsa_KO_ENTREZID", "hsa_pathwayCommons_ENSEMBL", "kegg_pathwayCommons", "KO_pathway.id", "KO_pathwayCommons", "mapping", "mmu_KO_ENSEMBL", "mmu_KO_ENTREZID", "mmu_pathwayCommons_ENSEMBL", "mmu_pathwayCommons_ENTREZID", "pathwayCommons_SYMBOL", "SYMBOL_pathway.id" ] }, { "page": "pathway.completeness.cutoff.info", "title": "Cutoffs of pathway completeness used for defining existance of pathway in a species", "topics": [ "pathway.completeness.cutoff.info" ] }, { "page": "pathway.species.pct_Mapped", "title": "Pathway completeness in a species", "topics": [ "pathway.species.pct_Mapped" ] }, { "page": "sbgn.xmls", "title": "XML code of a SBGN-ML file", "topics": [ "sbgn.xmls" ] } ], "_readme": "https://github.com/bioc/SBGNview.data/raw/RELEASE_3_23/README.md", "_rundeps": [ "base64enc", "bookdown", "bslib", "cachem", "cli", "digest", "evaluate", "fastmap", "fontawesome", "fs", "highr", "htmltools", "jquerylib", "jsonlite", "knitr", "lifecycle", "memoise", "mime", "R6", "rappdirs", "rlang", "rmarkdown", "sass", "tinytex", "xfun", "yaml" ], "_vignettes": [ { "source": "SBGNview.data.vignette.Rmd", "filename": "SBGNview.data.vignette.html", "title": "Supporting Datasets for SBGNview Package", "author": "Xiaoxi Dong, Kovidh Vegesna, kvegesna (AT) uncc.edu, Weijun Luo, luo_weijun (AT) yahoo.com", "engine": "knitr::rmarkdown", "headings": [ "Dataset: IFNg", "Dataset cancer.ds (GSE16873)", "ID mapping files", "Molecule (or gene) IDs to glyphs IDs in SBGN-ML files:", "Molecule (or gene) IDs to KEGG ortholog IDs", "Molecule (or gene) IDs to pathway IDs" ], "created": "2019-05-28 17:49:58", "modified": "2021-03-03 02:30:18", "commits": 4 } ], "_score": 4.477121254719663, "_indexed": false, "_nocasepkg": "sbgnview.data", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/SBGNview.data", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.26.0", "date": "2026-10-10T11:24:45.000Z", "distro": "resolute", "commit": "b1663a69ae087b9b61c3f2c8acf464d799eb7f5a", "fileid": "https://r2.ropensci.org/67903e0c2a5c24f2766747d3a974df0fc6562c3c12bff8508daa783fcfbac81a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047410779" }, { "r": "4.6.1", "os": "linux", "version": "1.26.0", "date": "2026-10-10T11:24:30.000Z", "distro": "resolute", "commit": "b1663a69ae087b9b61c3f2c8acf464d799eb7f5a", "fileid": "https://r2.ropensci.org/071b1bc51822679dfc5c84a0bbf9764461b14e35ad446e142fff47700157b971", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047410779" } ] }