{ "_id": "6aea7930818c9e3ef6dc045e", "Package": "enrichmet", "Type": "Package", "Title": "enrichmet: R package for Quick and Easy Pathway and Network\nAnalyses in Metabolomics", "Version": "0.99.18", "Authors@R": "c(\nperson(\"Yonatan\", \"Mekonnen\", email = \"yaayalew@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-7430-9428\")),\nperson(given = \"H. Lee Moffitt Cancer Center & Research Institute\",\nrole = \"fnd\",\ncomment = \"Grant number: P01CA250984\")\n)", "Description": "Provides functions to perform metabolite-based pathway\nenrichment analysis using Fisher's exact test and MetSEA.\nComputes relative betweenness centrality (RBC) of input\nmetabolites in a pathway-metabolite interaction network. The\npackage generates visualizations including pathway dot plots,\nMetSEA plots, metabolite centrality plots, and network plots.\nIt supports KEGG-based pathway inputs and generates exportable\nresults.", "License": "AGPL-3 + file LICENSE", "Encoding": "UTF-8", "URL": "https://github.com/biodatalab/enrichmet", "BugReports": "https://github.com/biodatalab/enrichmet/issues", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "biocViews": "Metabolomics, Pathways, Network, NetworkEnrichment, KEGG,\nVisualization", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libglpk-dev\nlibicu-dev libpng-dev libxml2-dev libssl-dev perl zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-10-09 22:56:28 UTC", "RemoteUrl": "https://github.com/bioc/enrichmet", "RemoteRef": "HEAD", "RemoteSha": "3141d808a3ce25660dfb0a6e4d2356cba929e0cd", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-03 23:42:30 UTC", "User": "root" }, "Author": "Yonatan Mekonnen [aut, cre] (ORCID:\n),\nH. Lee Moffitt Cancer Center & Research Institute [fnd] (Grant number:\nP01CA250984)", "Maintainer": "Yonatan Mekonnen ", "_user": "bioc", "_type": "src", "_file": "enrichmet_0.99.18.tar.gz", "_fileid": "https://r2.ropensci.org/be284f4db999dd4ca796c728f1b491552e7e23f2b6f9e5b163b5dff6578e877d", "_filesize": 2286567, "_sha256": "be284f4db999dd4ca796c728f1b491552e7e23f2b6f9e5b163b5dff6578e877d", "_expires": "2027-02-12T00:15:42.000Z", "_created": "2026-11-03T23:42:30.000Z", "_published": "2026-11-04T00:15:44.352Z", "_upstream": "https://github.com/bioc/enrichmet", "_status": "success", "_maintainer": { "name": "Yonatan Mekonnen", "email": "yaayalew@gmail.com", "login": "yonatan2627", "description": "", "uuid": 180336457, "orcid": "0000-0002-7430-9428" }, "_jobs": [ { "job": 126283309294, "time": 192, "config": "bioc-checks", "r": "4.6.2", "check": "NOTE", "artifact": "13281521035" }, { "job": 126283309087, "time": 505, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13281726879" }, { "job": 126283309169, "time": 515, "config": "linux-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13281447282" }, { "job": 126283309104, "time": 526, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "13283950434" }, { "job": 126283309176, "time": 361, "config": "macos-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13282973309" }, { "job": 126281142587, "time": 300, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13281825341" }, { "job": 126283309117, "time": 162, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13281660957" }, { "job": 126283309270, "time": 316, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13282080958" }, { "job": 126283309320, "time": 369, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "13282675576" }, { "job": 126283309586, "time": 380, "config": "windows-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13281193233" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41740654492", "_commit": { "id": "3141d808a3ce25660dfb0a6e4d2356cba929e0cd", "author": "Yonatan2627 ", "committer": "Yonatan2627 ", "message": "Update package DESCRIPTION\n", "time": 1791586588 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "BiocFileCache", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "circlize", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Imports" }, { "package": "curl", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "fgsea", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggraph", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "openxlsx", "role": "Imports" }, { "package": "qvalue", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.2.0", "role": "Suggests" }, { "package": "withr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-50", "n": 7 }, { "week": "2026-38", "n": 13 }, { "week": "2026-41", "n": 3 } ], "_tags": [], "_topics": [ "metabolomics", "pathways", "network", "networkenrichment", "kegg", "visualization" ], "_stars": 2, "_contributors": [ { "user": "yonatan2627", "count": 60, "uuid": 180336457 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 484, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/biodatalab/enrichmet", "_searchresults": 8, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/enrichmet.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "LICENSE" ], "_cranurl": false, "_exports": [ "calculate_metabolite_centrality", "create_centrality_plot", "create_enrichment_plot", "create_gsea_plot", "create_heatmap_plot", "create_impact_plot", "create_interaction_plot", "create_membership_plot", "create_network_plot", "da_results_from_se", "enrichmet", "extract_kegg_ids", "extract_measured_kegg_ids", "fetch_kegg_chebi", "fetch_kegg_compound_lookup", "fetch_kegg_pathway_metabolites", "fetch_kegg_reactome", "fetch_lion_lipid_ontology", "fetch_reactome_reactions", "get_cached_file", "perform_enrichment_analysis", "perform_enrichment_analysis_bg", "perform_gsea_analysis", "prepare_gmt_data", "run_de" ], "_help": [ { "page": "calculate_metabolite_centrality", "title": "Calculate Metabolite Centrality", "topics": [ "calculate_metabolite_centrality" ] }, { "page": "create_centrality_plot", "title": "Create Centrality Plot", "topics": [ "create_centrality_plot" ] }, { "page": "create_enrichment_plot", "title": "Create Pathway Enrichment Plot", "topics": [ "create_enrichment_plot" ] }, { "page": "create_gsea_plot", "title": "Create GSEA Plot", "topics": [ "create_gsea_plot" ] }, { "page": "create_heatmap_plot", "title": "Create Enrichment Heatmap", "topics": [ "create_heatmap_plot" ] }, { "page": "create_impact_plot", "title": "Create Impact vs Significance Plot", "topics": [ "create_impact_plot" ] }, { "page": "create_interaction_plot", "title": "Create Metabolite Interaction Network (Reactome)", "topics": [ "create_interaction_plot" ] }, { "page": "create_membership_plot", "title": "Create Pathway Membership Plot", "topics": [ "create_membership_plot" ] }, { "page": "create_network_plot", "title": "Create Metabolite Pathway Network", "topics": [ "create_network_plot" ] }, { "page": "da_results_from_se", "title": "Convert a SummarizedExperiment to a da_results Object", "topics": [ "da_results_from_se" ] }, { "page": "enrichmet", "title": "ENRICHMET: Comprehensive Pathway Analysis for Metabolomics Data", "topics": [ "enrichmet" ] }, { "page": "extract_kegg_ids", "title": "Extract KEGG compound IDs from pathway data", "topics": [ "extract_kegg_ids" ] }, { "page": "extract_measured_kegg_ids", "title": "Extract measured KEGG metabolite IDs from a summary statistics table", "topics": [ "extract_measured_kegg_ids" ] }, { "page": "fetch_kegg_chebi", "title": "Fetch KEGG-ChEBI mappings", "topics": [ "fetch_kegg_chebi" ] }, { "page": "fetch_kegg_compound_lookup", "title": "Fetch KEGG compound names", "topics": [ "fetch_kegg_compound_lookup" ] }, { "page": "fetch_kegg_pathway_metabolites", "title": "Fetch KEGG pathway-metabolite relationships", "topics": [ "fetch_kegg_pathway_metabolites" ] }, { "page": "fetch_kegg_reactome", "title": "Build KEGG-Reactome reaction mappings", "topics": [ "fetch_kegg_reactome" ] }, { "page": "fetch_lion_lipid_ontology", "title": "Fetch LION lipid ontology", "topics": [ "fetch_lion_lipid_ontology" ] }, { "page": "fetch_reactome_reactions", "title": "Fetch Reactome reactions", "topics": [ "fetch_reactome_reactions" ] }, { "page": "get_cached_file", "title": "Download and cache a remote file", "topics": [ "get_cached_file" ] }, { "page": "perform_enrichment_analysis", "title": "Perform Pathway Enrichment Analysis", "topics": [ "perform_enrichment_analysis" ] }, { "page": "perform_enrichment_analysis_bg", "title": "Perform pathway enrichment with optional background correction", "topics": [ "perform_enrichment_analysis_bg" ] }, { "page": "perform_gsea_analysis", "title": "Perform GSEA-style Pathway Enrichment Analysis", "topics": [ "perform_gsea_analysis" ] }, { "page": "prepare_gmt_data", "title": "Prepare GMT Data for Pathway Analysis", "topics": [ "prepare_gmt_data" ] }, { "page": "run_de", "title": "Run Differential Expression Analysis using LIMMA", "topics": [ "run_de" ] } ], "_rundeps": [ "abind", "askpass", "base64enc", "BH", "Biobase", "BiocFileCache", "BiocGenerics", "BiocParallel", "bit", "bit64", "blob", "cachem", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "cowplot", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "digest", "doParallel", "dplyr", "farver", "fastmap", "fastmatch", "fgsea", "filelock", "foreach", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "GetoptLong", "ggforce", "ggplot2", "ggraph", "ggrepel", "GlobalOptions", "glue", "graphlayouts", "gridExtra", "gtable", "httr2", "igraph", "IRanges", "isoband", "iterators", "jsonlite", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "openssl", "openxlsx", "pillar", "pkgconfig", "plyr", "png", "polyclip", "purrr", "qvalue", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape2", "rjson", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "shape", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "systemfonts", "tibble", "tidygraph", "tidyr", "tidyselect", "tweenr", "utf8", "vctrs", "viridis", "viridisLite", "withr", "XVector", "zip" ], "_vignettes": [ { "source": "Tutorial.Rmd", "filename": "Tutorial.html", "title": "enrichmet: Pathway and Network Analysis for Metabolomics Tutorial", "author": "Yonatan Ayalew Mekonnen", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Input requirements", "Query metabolites", "Summary statistics (optional but required for MetSEA)", "Pathway–metabolite map", "Case study", "Background-corrected enrichment", "Network centrality", "Visualisations", "Differential analysis followed by enrichment", "Using a SummarizedExperiment as input", "Application to a lipid pathway map", "Bibliography", "Session information" ], "created": "2025-05-23 19:59:20", "modified": "2026-10-06 18:20:00", "commits": 19 } ], "_score": 2.778151250383644, "_indexed": true, "_nocasepkg": "enrichmet", "_universes": [ "bioc", "yonatan2627", "biodatalab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.18", "date": "2026-11-03T23:46:57.000Z", "distro": "resolute", "commit": "3141d808a3ce25660dfb0a6e4d2356cba929e0cd", "fileid": "https://r2.ropensci.org/e5a62d74afdb961a616f2cf97e837cb1018b72ff8033b14759842940550d3dcb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41740654492" }, { "r": "4.6.2", "os": "linux", "version": "0.99.18", "date": "2026-11-03T23:46:56.000Z", "distro": "resolute", "commit": "3141d808a3ce25660dfb0a6e4d2356cba929e0cd", "fileid": "https://r2.ropensci.org/d982a7fe2e6fcddaa84e8b5419ffb076d3e4d0a5cafb61b8b7a8dd21f15a9a2d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41740654492" }, { "r": "4.5.3", "os": "mac", "version": "0.99.18", "date": "2026-11-04T00:08:51.000Z", "commit": "3141d808a3ce25660dfb0a6e4d2356cba929e0cd", "fileid": "https://r2.ropensci.org/adb5eb8000e3a7c386750a77a460929bea268e14b6e630d86d73b1ecc1f75e88", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41740654492" }, { "r": "4.6.2", "os": "mac", "version": "0.99.18", "date": "2026-11-04T00:08:53.000Z", "commit": "3141d808a3ce25660dfb0a6e4d2356cba929e0cd", "fileid": "https://r2.ropensci.org/1d66976be7ef6703cb632f73318170434e0d0ad2421a50c573558f847be50da2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41740654492" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.18", "date": "2026-11-03T23:45:37.000Z", "commit": "3141d808a3ce25660dfb0a6e4d2356cba929e0cd", "fileid": "https://r2.ropensci.org/793d710931d49ed834226169dcb14bc7d4d66573d9e31b348b03664b66ee8825", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41740654492" }, { "r": "4.7.0", "os": "win", "version": "0.99.18", "date": "2026-11-03T23:44:01.000Z", "commit": "3141d808a3ce25660dfb0a6e4d2356cba929e0cd", "fileid": "https://r2.ropensci.org/5007f04ce53d3a2abb6e2b666c49e34b55a1ff763ad662859eaf5884724343a6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41740654492" }, { "r": "4.5.3", "os": "win", "version": "0.99.18", "date": "2026-11-03T23:44:19.000Z", "commit": "3141d808a3ce25660dfb0a6e4d2356cba929e0cd", "fileid": "https://r2.ropensci.org/faadf3dc7942097629200578d2cc9c45d10e095cbc578c368c5e399f57a3139f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41740654492" }, { "r": "4.6.2", "os": "win", "version": "0.99.18", "date": "2026-11-03T23:44:22.000Z", "commit": "3141d808a3ce25660dfb0a6e4d2356cba929e0cd", "fileid": "https://r2.ropensci.org/b8515fd96488c021fda5d33623e2a946e31bfb9d9abe75ecd24e377f79ffdede", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41740654492" } ] }