{ "_id": "6ac03b5691601a2ad2996462", "Package": "punKEGGer", "Title": "Parse, Expand, Annotate and Visualize KEGG Pathway Networks as\nTidy Graphs", "Version": "0.99.65", "Authors@R": "person(given = \"Guillermo\",\nfamily = \"de Anda Jáuregui\",\nemail = \"gdeanda@inmegen.edu.mx\",\nrole = c(\"aut\", \"cre\"))", "Description": "Provides tools to parse KEGG pathway KGML files into tidy\ngraphs, expand metanodes (e.g., multi-gene entries), annotate\nthem with custom dictionaries, and produce consistent\nvisualizations using ggraph. Enables integration of KEGG\npathways with tidygraph-based workflows.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "biocViews": "Pathways, GraphAndNetwork, Software, Network, Visualization,\nKEGG", "URL": "https://github.com/guillermodeandajauregui/punKEGGer", "BugReports": "https://github.com/guillermodeandajauregui/punKEGGer/issues", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libglpk-dev\nlibicu-dev libpng-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-07-10 20:01:12 UTC", "RemoteUrl": "https://github.com/bioc/punKEGGer", "RemoteRef": "HEAD", "RemoteSha": "68a8e2d60f6fc03ee0496bbbfafc65f3b11fdebe", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-02 23:10:35 UTC", "User": "root" }, "Author": "Guillermo de Anda Jáuregui [aut, cre]", "Maintainer": "Guillermo de Anda Jáuregui ", "_user": "bioc", "_type": "src", "_file": "punKEGGer_0.99.65.tar.gz", "_fileid": "https://r2.ropensci.org/94676a468c08faaed237891518c1185061edd05be8c100ae823e8d0ec22f75de", "_filesize": 2405382, "_sha256": "94676a468c08faaed237891518c1185061edd05be8c100ae823e8d0ec22f75de", "_expires": "2027-01-10T23:16:35.000Z", "_created": "2026-10-02T23:10:35.000Z", "_published": "2026-10-02T23:16:38.070Z", "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37075954171", "_status": "success", "_upstream": "https://github.com/bioc/punKEGGer", "_commit": { "id": "68a8e2d60f6fc03ee0496bbbfafc65f3b11fdebe", "author": "gdj ", "committer": "gdj ", "message": "modified vignette, to be less barebones\n", "time": 1783713672 }, "_maintainer": { "name": "Guillermo de Anda Jáuregui", "email": "gdeanda@inmegen.edu.mx", "login": "guillermodeandajauregui", "description": "", "uuid": 7853392 }, "_distro": "resolute", "_jobs": [ { "job": 111066944991, "time": 196, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11256737835" }, { "job": 111066945022, "time": 311, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11256728042" }, { "job": 111066945005, "time": 272, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11256343556" }, { "job": 111066945016, "time": 212, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11256313520" }, { "job": 111066945068, "time": 168, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11257425536" }, { "job": 111066021866, "time": 215, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11256527452" }, { "job": 111066944977, "time": 128, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11257465277" }, { "job": 111066945055, "time": 89, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11256542789" }, { "job": 111066945082, "time": 101, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11256368084" }, { "job": 111066945087, "time": 101, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11257435404" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggraph", "role": "Imports" }, { "package": "glue", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidygraph", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "KEGGREST", "role": "Imports" }, { "package": "xml2", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "XML", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-14", "n": 3 }, { "week": "2026-28", "n": 24 } ], "_tags": [], "_topics": [ "pathways", "graphandnetwork", "software", "network", "visualization", "kegg" ], "_stars": 1, "_contributors": [ { "user": "guillermodeandajauregui", "count": 76, "uuid": 7853392 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 470, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/guillermodeandajauregui/punkegger", "_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/punKEGGer.html", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_cranurl": false, "_exports": [ "add_kegg_layout", "annotate_kegg_graph", "combine_kegg_network", "create_meta_dict", "expand_metagraph", "extract_kegg_nodes", "fetch_kegg_kgml", "layout_kegg", "parse_kegg_groups", "parse_kegg_relations_clean", "plot_kegg_graph" ], "_help": [ { "page": "add_kegg_layout", "title": "Add KEGG layout coordinates to a tidygraph", "topics": [ "add_kegg_layout" ] }, { "page": "annotate_kegg_graph", "title": "Annotate a KEGG tidygraph with custom identifiers", "topics": [ "annotate_kegg_graph" ] }, { "page": "combine_kegg_network", "title": "Combine KEGG group and relation edges into a tidygraph", "topics": [ "combine_kegg_network" ] }, { "page": "create_meta_dict", "title": "Create a meta_id-to-annotation dictionary", "topics": [ "create_meta_dict" ] }, { "page": "expand_metagraph", "title": "Expand a KEGG tidygraph by unrolling multi-gene metanodes", "topics": [ "expand_metagraph" ] }, { "page": "extract_kegg_nodes", "title": "Extract KEGG node information from a KGML file", "topics": [ "extract_kegg_nodes" ] }, { "page": "fetch_kegg_kgml", "title": "Fetch a KEGG pathway KGML via KEGGREST", "topics": [ "fetch_kegg_kgml" ] }, { "page": "layout_kegg", "title": "Extract node layout coordinates from a KEGG KGML file", "topics": [ "layout_kegg" ] }, { "page": "parse_kegg_groups", "title": "Parse KEGG group nodes from a KGML file", "topics": [ "parse_kegg_groups" ] }, { "page": "parse_kegg_relations_clean", "title": "Parse clean KEGG relations from a KGML file", "topics": [ "parse_kegg_relations_clean" ] }, { "page": "plot_kegg_graph", "title": "Visualize a KEGG pathway tidygraph using manual layout", "topics": [ "plot_kegg_graph" ] } ], "_pkglogo": "https://github.com/bioc/punKEGGer/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/bioc/punKEGGer/raw/HEAD/README.md", "_rundeps": [ "askpass", "base64enc", "BiocGenerics", "Biostrings", "cachem", "cli", "cpp11", "crayon", "curl", "dplyr", "farver", "fastmap", "generics", "ggforce", "ggplot2", "ggraph", "ggrepel", "glue", "graphlayouts", "gridExtra", "gtable", "httr", "igraph", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "polyclip", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "S4Vectors", "S7", "scales", "Seqinfo", "stringi", "stringr", "sys", "systemfonts", "tibble", "tidygraph", "tidyr", "tidyselect", "tweenr", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xml2", "XVector" ], "_vignettes": [ { "source": "punkegger-vignette-bioconductor.Rmd", "filename": "punkegger-vignette-bioconductor.html", "title": "punKEGGer: parsing and visualization of KEGG pathways for network science", "author": "Guillermo de Anda Jáuregui", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Example 1: Parse a single KEGG pathway", "Example 2: Add gene annotations", "Example 3: Visualize your pathway", "Alternative layout using ggraph:", "Example 4: Combine pathways and connect to your network science pipeline" ], "created": "2025-07-22 05:13:48", "modified": "2026-07-10 20:01:12", "commits": 8 } ], "_score": 3, "_indexed": true, "_nocasepkg": "punkegger", "_universes": [ "bioc", "guillermodeandajauregui" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.65", "date": "2026-10-02T23:15:39.000Z", "distro": "resolute", "commit": "68a8e2d60f6fc03ee0496bbbfafc65f3b11fdebe", "fileid": "https://r2.ropensci.org/9cf1417a806d566051dbb1023832df7cf5abdbcedc5c3321e426a1e0915b099c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37075954171" }, { "r": "4.6.1", "os": "linux", "version": "0.99.65", "date": "2026-10-02T23:14:55.000Z", "distro": "resolute", "commit": "68a8e2d60f6fc03ee0496bbbfafc65f3b11fdebe", "fileid": "https://r2.ropensci.org/b924578d9d02bcfc5754c653bb4cd1c96553fbd5d71956a71b2907614a818e87", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37075954171" }, { "r": "4.5.3", "os": "mac", "version": "0.99.65", "date": "2026-10-02T23:14:03.000Z", "commit": "68a8e2d60f6fc03ee0496bbbfafc65f3b11fdebe", "fileid": "https://r2.ropensci.org/0fa3299568de4733786b7c947a9dfdfa457483e4fb0d7bad006d6fe53682240e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37075954171" }, { "r": "4.6.1", "os": "mac", "version": "0.99.65", "date": "2026-10-02T23:13:24.000Z", "commit": "68a8e2d60f6fc03ee0496bbbfafc65f3b11fdebe", "fileid": "https://r2.ropensci.org/6017092f5c419a4fa88c303d0269b86064f7ed3d5d863894061a4b16bfcfe684", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37075954171" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.65", "date": "2026-10-02T23:13:38.000Z", "commit": "68a8e2d60f6fc03ee0496bbbfafc65f3b11fdebe", "fileid": "https://r2.ropensci.org/4a4510b98da2cd1df348bad864ceb93cfee8f8ff9bfe3ada959c6952398640dc", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37075954171" }, { "r": "4.7.0", "os": "win", "version": "0.99.65", "date": "2026-10-02T23:11:47.000Z", "commit": "68a8e2d60f6fc03ee0496bbbfafc65f3b11fdebe", "fileid": "https://r2.ropensci.org/114f9f4a75d2d26085f6542b6ce5ba3527d30977e922cbd2fac2513f9c5b2679", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37075954171" }, { "r": "4.5.3", "os": "win", "version": "0.99.65", "date": "2026-10-02T23:12:05.000Z", "commit": "68a8e2d60f6fc03ee0496bbbfafc65f3b11fdebe", "fileid": "https://r2.ropensci.org/7a1de958d9fb9011992617ca75ef5ba53eb9571315a28a3cb6f6f5661ec421a9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37075954171" }, { "r": "4.6.1", "os": "win", "version": "0.99.65", "date": "2026-10-02T23:12:01.000Z", "commit": "68a8e2d60f6fc03ee0496bbbfafc65f3b11fdebe", "fileid": "https://r2.ropensci.org/2cb4cd3aa7cd2e947da7d60df022de98ff5b3fbf60a2eb25e6d16ba295e37604", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37075954171" } ] }