{ "_id": "6a168eccacfb0bcc41d77dc5", "Package": "iSEEpathways", "Title": "iSEE extension for panels related to pathway analysis", "Version": "1.10.0", "Date": "2024-10-01", "Authors@R": "c(person(\"Kevin\", \"Rue-Albrecht\", email = \"kevinrue67@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3899-3872\")),\nperson(\"Thomas\", \"Sandmann\", email = \"tomsing1@gmail.com\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-6601-8890\")),\nperson(\"Charlotte\", \"Soneson\", role=\"aut\", email=\"charlottesoneson@gmail.com\",\ncomment = c(ORCID = '0000-0003-3833-2169')),\nperson(\"Federico\", \"Marini\", role=\"ctb\", email=\"marinif@uni-mainz.de\",\ncomment = c(ORCID = '0000-0003-3252-7758')),\nperson(\"Denali Therapeutics\", role = c(\"fnd\")))", "Description": "This package contains diverse functionality to extend the\nusage of the iSEE package, including additional classes for the\npanels or modes facilitating the analysis of pathway analysis\nresults. This package does not perform pathway analysis.\nInstead, it provides methods to embed precomputed pathway\nanalysis results in a SummarizedExperiment object, in a manner\nthat is compatible with interactive visualisation in iSEE\napplications.", "License": "Artistic-2.0", "URL": "https://github.com/iSEE/iSEEpathways", "BugReports": "https://support.bioconductor.org/t/iSEEpathways", "biocViews": "Software, Infrastructure, DifferentialExpression,\nGeneExpression, GUI, Visualization, Pathways,\nGeneSetEnrichment, GO, ShinyApps", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libglpk-dev make libpng-dev libuv1-dev\nlibxml2-dev perl zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:01:27 UTC", "RemoteUrl": "https://github.com/bioc/iSEEpathways", "RemoteRef": "RELEASE_3_23", "RemoteSha": "8457a7639360e2008f36d691b9eff1ee6fc683d1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-27 06:18:12 UTC", "User": "root" }, "Author": "Kevin Rue-Albrecht [aut, cre] (ORCID:\n),\nThomas Sandmann [ctb] (ORCID: ),\nCharlotte Soneson [aut] (ORCID:\n),\nFederico Marini [ctb] (ORCID: ),\nDenali Therapeutics [fnd]", "Maintainer": "Kevin Rue-Albrecht ", "MD5sum": "c8bedaf1e243484d4932d6983cd06b39", "_user": "bioc-release", "_type": "src", "_file": "iSEEpathways_1.10.0.tar.gz", "_fileid": "1be545a2845226c1b6493b2f9657b305edcb932263725d4a25cf5c20bde8b0b4", "_filesize": 1493720, "_sha256": "1be545a2845226c1b6493b2f9657b305edcb932263725d4a25cf5c20bde8b0b4", "_created": "2026-05-27T06:18:12.000Z", "_published": "2026-05-27T06:27:24.544Z", "_jobs": [ { "job": 78019138587, "time": 271, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7233326512" }, { "job": 78019138619, "time": 412, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7233361202" }, { "job": 78019138617, "time": 411, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7233360936" }, { "job": 78019138598, "time": 217, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7233312820" }, { "job": 78019138582, "time": 269, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7233326033" }, { "job": 78018303632, "time": 424, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7233262585" }, { "job": 78019138601, "time": 239, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7233318144" }, { "job": 78019138633, "time": 441, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7233369112" }, { "job": 78019138615, "time": 443, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7233369319" }, { "job": 78019138605, "time": 493, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7233382040" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494159720", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/iSEEpathways", "_commit": { "id": "8457a7639360e2008f36d691b9eff1ee6fc683d1", "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": 1777381287 }, "_maintainer": { "name": "Kevin Rue-Albrecht", "email": "kevinrue67@gmail.com", "login": "kevinrue", "mastodon": "@kevinrue@fosstodon.org", "orcid": "0000-0003-3899-3872", "description": "Ingénieur diplômé;\nComputational Biologist; \nSoftware engineer;\nBioconductor contributor", "uuid": 5769108 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "iSEE", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "shinyWidgets", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "airway", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "edgeR", "role": "Suggests" }, { "package": "fgsea", "role": "Suggests" }, { "package": "GO.db", "role": "Suggests" }, { "package": "iSEEde", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "RefManageR", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "scater", "role": "Suggests" }, { "package": "scuttle", "role": "Suggests" }, { "package": "sessioninfo", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.11.0", "bioc": "3.24" }, { "branch": "release", "version": "1.10.0", "bioc": "3.23" } ], "_topics": [ "software", "infrastructure", "differentialexpression", "geneexpression", "gui", "visualization", "pathways", "genesetenrichment", "go", "shinyapps", "bioconductor", "hacktoberfest", "isee", "iseeu" ], "_stars": 1, "_contributors": [ { "user": "kevinrue", "count": 31, "uuid": 5769108 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 }, { "user": "csoneson", "count": 1, "uuid": 5628952 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 260, "source": "https://www.bioconductor.org/packages/stats/bioc/iSEEpathways" }, "_devurl": "https://github.com/isee/iseepathways", "_searchresults": 13, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/iSEEpathways.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/isee/iseepathways", "_realowner": "bioc", "_cranurl": false, "_exports": [ ".cacheCommonInfo", ".createObservers", ".defineDataInterface", ".defineInterface", ".defineOutput", ".fullName", ".generateOutput", ".generateTable", ".isBrushable", ".multiSelectionActive", ".multiSelectionCommands", ".multiSelectionDimension", ".panelColor", ".refineParameters", ".renderOutput", ".showSelectionDetails", "embedPathwaysResults", "embedPathwaysResultsMethods", "featuresStats", "FgseaEnrichmentPlot", "initialize", "iSEEfgseaResults", "pathwaysList", "pathwaysResults", "pathwaysResultsNames", "PathwaysTable", "pathwayType", "simulateExampleData" ], "_help": [ { "page": "FgseaEnrichmentPlot-class", "title": "The FgseaEnrichmentPlot class", "topics": [ ".cacheCommonInfo,FgseaEnrichmentPlot-method", ".createObservers,FgseaEnrichmentPlot-method", ".defineDataInterface,FgseaEnrichmentPlot-method", ".defineInterface,FgseaEnrichmentPlot-method", ".defineOutput,FgseaEnrichmentPlot-method", ".fullName,FgseaEnrichmentPlot-method", ".generateOutput,FgseaEnrichmentPlot-method", ".isBrushable,FgseaEnrichmentPlot-method", ".multiSelectionActive,FgseaEnrichmentPlot-method", ".multiSelectionCommands,FgseaEnrichmentPlot-method", ".multiSelectionDimension,FgseaEnrichmentPlot-method", ".panelColor,FgseaEnrichmentPlot-method", ".refineParameters,FgseaEnrichmentPlot-method", ".renderOutput,FgseaEnrichmentPlot-method", ".showSelectionDetails,FgseaEnrichmentPlot-method", "FgseaEnrichmentPlot", "FgseaEnrichmentPlot-class", "initialize,FgseaEnrichmentPlot-method" ] }, { "page": "iSEEfgseaResults-class", "title": "The iSEEfgseaResults class", "topics": [ "embedPathwaysResults,iSEEfgseaResults-method", "featuresStats,iSEEfgseaResults-method", "iSEEfgseaResults", "iSEEfgseaResults-class", "pathwaysList,iSEEfgseaResults-method", "pathwayType,iSEEfgseaResults-method" ] }, { "page": "iSEEpathwaysResults-class", "title": "The iSEEpathwaysResults class", "topics": [ "iSEEpathwaysResults", "iSEEpathwaysResults-class", "show,iSEEpathwaysResults-method" ] }, { "page": "pathway-generics", "title": "Generics for Pathway Analysis Results", "topics": [ "featuresStats", "pathway-generics", "pathwaysList", "pathwayType" ] }, { "page": "pathwaysResults", "title": "Extract contrast results embedded in a SummarizedExperiment object", "topics": [ "pathwaysResults", "pathwaysResultsNames" ] }, { "page": "PathwaysTable-class", "title": "The PathwaysTable class", "topics": [ ".cacheCommonInfo,PathwaysTable-method", ".createObservers,PathwaysTable-method", ".defineDataInterface,PathwaysTable-method", ".defineInterface,PathwaysTable-method", ".fullName,PathwaysTable-method", ".generateTable,PathwaysTable-method", ".multiSelectionActive,PathwaysTable-method", ".multiSelectionCommands,PathwaysTable-method", ".multiSelectionDimension,PathwaysTable-method", ".panelColor,PathwaysTable-method", ".refineParameters,PathwaysTable-method", ".showSelectionDetails,PathwaysTable-method", "initialize,PathwaysTable-method", "PathwaysTable", "PathwaysTable-class" ] }, { "page": "simulateExampleData", "title": "Simulate Example Data", "topics": [ "simulateExampleData" ] }, { "page": "utils-SummarizedExperiment", "title": "Generics for Embbedding Pathway Analysis Results into a SummarizedExperiment Object", "topics": [ "embedPathwaysResults", "embedPathwaysResults,data.frame-method", "embedPathwaysResultsMethods", "utils-SummarizedExperiment" ] } ], "_readme": "https://github.com/bioc/iSEEpathways/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "base64enc", "Biobase", "BiocGenerics", "bslib", "cachem", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "colourpicker", "commonmark", "ComplexHeatmap", "cpp11", "crayon", "crosstalk", "DelayedArray", "digest", "doParallel", "DT", "evaluate", "farver", "fastmap", "fontawesome", "foreach", "fs", "generics", "GenomicRanges", "GetoptLong", "ggplot2", "ggrepel", "GlobalOptions", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "httpuv", "igraph", "IRanges", "iSEE", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "listviewer", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "miniUI", "nlme", "otel", "pkgconfig", "png", "promises", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rintrojs", "rjson", "rlang", "rmarkdown", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "shape", "shiny", "shinyAce", "shinydashboard", "shinyjs", "shinyWidgets", "SingleCellExperiment", "sourcetools", "SparseArray", "SummarizedExperiment", "tinytex", "vctrs", "vipor", "viridisLite", "withr", "xfun", "xtable", "XVector", "yaml" ], "_vignettes": [ { "source": "integration.Rmd", "filename": "integration.html", "title": "Integration with other panels", "author": "Kevin Rue-Albrecht", "engine": "knitr::rmarkdown", "headings": [ "Scenario", "Demonstration", "Example data", "Experimental metadata", "Feature identifiers", "Gene expression", "Differential expression analysis", "Pathways", "Mapping pathways to genes", "Gene set enrichment analysis", "Displaying additional pathway information", "Live app", "Trading off memory usage for speed", "Reproducibility", "Bibliography" ], "created": "2023-02-16 09:40:45", "modified": "2023-09-04 10:41:42", "commits": 9 }, { "source": "iSEEpathways.Rmd", "filename": "iSEEpathways.html", "title": "Introduction to iSEEpathways", "author": "Kevin Rue-Albrecht", "engine": "knitr::rmarkdown", "headings": [ "Basics", "Install iSEEpathways", "Required knowledge", "Asking for help", "Citing iSEEpathways", "Quick start to using to iSEEpathways", "Reproducibility", "Bibliography" ], "created": "2022-12-02 14:33:14", "modified": "2023-09-21 10:41:12", "commits": 9 }, { "source": "gene-ontology.Rmd", "filename": "gene-ontology.html", "title": "Working with the Gene Ontology", "author": "Kevin Rue-Albrecht", "engine": "knitr::rmarkdown", "headings": [ "Scenario", "Demonstration", "Example data", "Pathway information", "Live app", "Reproducibility", "Bibliography" ], "created": "2023-02-16 09:40:45", "modified": "2023-09-04 10:41:42", "commits": 5 } ], "_score": 4.892094602690481, "_indexed": false, "_nocasepkg": "iseepathways", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/iSEEpathways", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.10.0", "date": "2026-05-27T06:22:51.000Z", "distro": "noble", "commit": "8457a7639360e2008f36d691b9eff1ee6fc683d1", "fileid": "a53c7bf4f7b7c3017bc8c7e0f07ea76d603c907c14b52e2e1aabce8780592dcd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494159720" }, { "r": "4.6.0", "os": "linux", "version": "1.10.0", "date": "2026-05-27T06:22:56.000Z", "distro": "noble", "commit": "8457a7639360e2008f36d691b9eff1ee6fc683d1", "fileid": "b7dece971d70d3564a3da45c0608fb36afae5be45ad85f22aa5b3b68719573e4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494159720" }, { "r": "4.5.3", "os": "mac", "version": "1.10.0", "date": "2026-05-27T06:20:46.000Z", "commit": "8457a7639360e2008f36d691b9eff1ee6fc683d1", "fileid": "16b35e4aaff50bc0e58a4953733eae96f5764a26824c60e90ccb041f9a5f7325", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494159720" }, { "r": "4.6.0", "os": "mac", "version": "1.10.0", "date": "2026-05-27T06:21:20.000Z", "commit": "8457a7639360e2008f36d691b9eff1ee6fc683d1", "fileid": "2c832fcd5f16530c1bcc8319503f20645e0d78bff8b8bda07d695fceaa222512", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494159720" }, { "r": "4.6.0", "os": "wasm", "version": "1.10.0", "date": "2026-05-27T06:22:45.000Z", "commit": "8457a7639360e2008f36d691b9eff1ee6fc683d1", "fileid": "3dac1ff09e46da921a35ebf78ecb96d2d45a880118d2f19c427c13f98259dcb2", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494159720" }, { "r": "4.7.0", "os": "win", "version": "1.10.0", "date": "2026-05-27T06:23:42.000Z", "commit": "8457a7639360e2008f36d691b9eff1ee6fc683d1", "fileid": "188cd7c77fccf01f7a6b76f2906898b23f7abe01c59c7933d65e62dae4c66bba", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494159720" }, { "r": "4.5.3", "os": "win", "version": "1.10.0", "date": "2026-05-27T06:23:39.000Z", "commit": "8457a7639360e2008f36d691b9eff1ee6fc683d1", "fileid": "305e53cafcaea1aede65560530d51162cc1c1b821f25f1cba949fe6d0c4e98a7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494159720" }, { "r": "4.6.0", "os": "win", "version": "1.10.0", "date": "2026-05-27T06:24:10.000Z", "commit": "8457a7639360e2008f36d691b9eff1ee6fc683d1", "fileid": "ef1f631135e2c57302cc2a5f22f60bc1ffa3cb080ba4b799e2061c73606cf78b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494159720" } ] }