{ "_id": "6a46d8d36527f6f71f9f6184", "Package": "enrichit", "Title": "'C++' Implementations of Functional Enrichment Analysis", "Version": "0.2.0", "Authors@R": "person(given = \"Guangchuang\", family = \"Yu\",\nemail = \"guangchuangyu@gmail.com\", role = c(\"aut\", \"cre\"))", "Maintainer": "Guangchuang Yu ", "Description": "Fast implementations of functional enrichment analysis\nmethods using 'C++' via 'Rcpp'. Currently provides\nOver-Representation Analysis (ORA), Gene Set Enrichment\nAnalysis (GSEA), Weighted Enrichment Analysis for ORA and GSEA,\nNetwork-based Set Enrichment Analysis (NSEA), multi-layer\nnetwork-based enrichment, and multi-omics integration\nworkflows. Additional features include early fusion at the\nfeature level, late fusion at the pathway level, multi-omics\ncontribution tracing, topology-aware explanation helpers,\nBayesian term selection, and extremely fast Random Walk with\nRestart (RWR) using 'RcppEigen'. The enrichment methods build\non GSEA by Subramanian et al. (2005)\n, the multilevel strategy derived\nfrom 'fgsea' by Korotkevich et al. (2021) ,\nand network-based enrichment ideas described by Glaab et al.\n(2012) .", "License": "Artistic-2.0", "Encoding": "UTF-8", "URL": "https://yulab-smu.top/biomedical-knowledge-mining-book/", "Config/roxygen2/version": "8.0.0", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-02 21:26:18 UTC", "User": "root" }, "Author": "Guangchuang Yu [aut, cre]", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-07-01 22:50:15 UTC", "RemoteUrl": "https://github.com/cran/enrichit", "RemoteRef": "HEAD", "RemoteSha": "fb787911b606956438ea0245139709d1adc5214d", "_user": "cran", "_type": "src", "_file": "enrichit_0.2.0.tar.gz", "_fileid": "https://r2.ropensci.org/a082534b0cf7ab24a8832507cd73bfa275869ef60e3e761154daf72ede86947e", "_filesize": 237804, "_sha256": "a082534b0cf7ab24a8832507cd73bfa275869ef60e3e761154daf72ede86947e", "_expires": "2026-10-10T21:32:03.000Z", "_created": "2026-07-02T21:26:18.000Z", "_published": "2026-07-02T21:32:03.954Z", "_jobs": [ { "job": 84881888645, "time": 247, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8052095623" }, { "job": 84881888626, "time": 221, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8052085685" }, { "job": 84881888631, "time": 200, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8052079252" }, { "job": 84881888601, "time": 278, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8052105343" }, { "job": 84881006373, "time": 306, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8052010556" }, { "job": 84881888595, "time": 225, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8052086697" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cran/actions/runs/28622371279", "_status": "success", "_upstream": "https://github.com/cran/enrichit", "_commit": { "id": "fb787911b606956438ea0245139709d1adc5214d", "author": "Guangchuang Yu ", "committer": "cran-robot ", "message": "version 0.2.0\n", "time": 1782946215 }, "_maintainer": { "name": "Guangchuang Yu", "email": "guangchuangyu@gmail.com", "login": "guangchuangyu", "twitter": "@guangchuangyu", "description": "Professor of Bioinformatics at Southern Medical University.", "uuid": 626539 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.0.10", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "yulab.utils", "version": "> 0.2.1", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Suggests" }, { "package": "BiasedUrn", "role": "Suggests" }, { "package": "clusterProfiler", "role": "Suggests" }, { "package": "DOSE", "role": "Suggests" }, { "package": "fgsea", "role": "Suggests" }, { "package": "gson", "role": "Suggests" }, { "package": "qvalue", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 65, "_updates": [ { "week": "2025-52", "n": 1 }, { "week": "2026-02", "n": 1 }, { "week": "2026-03", "n": 1 }, { "week": "2026-06", "n": 1 }, { "week": "2026-09", "n": 1 }, { "week": "2026-11", "n": 1 }, { "week": "2026-15", "n": 1 }, { "week": "2026-25", "n": 1 }, { "week": "2026-27", "n": 1 } ], "_tags": [ { "name": "0.0.8", "date": "2025-12-22" }, { "name": "0.0.9", "date": "2026-01-10" }, { "name": "0.1.0", "date": "2026-01-18" }, { "name": "0.1.1", "date": "2026-02-02" }, { "name": "0.1.2", "date": "2026-02-26" }, { "name": "0.1.3", "date": "2026-03-10" }, { "name": "0.1.4", "date": "2026-04-08" }, { "name": "0.1.5", "date": "2026-06-16" }, { "name": "0.2.0", "date": "2026-07-01" } ], "_stars": 0, "_contributors": [ { "user": "guangchuangyu", "count": 9, "uuid": 626539 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 615, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 18770, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/enrichit" }, "_searchresults": 21, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/enrichit.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "guangchuangyu", "_cranurl": false, "_releases": [ { "version": "0.0.8", "date": "2025-12-22" }, { "version": "0.0.9", "date": "2026-01-10" }, { "version": "0.1.0", "date": "2026-01-18" }, { "version": "0.1.1", "date": "2026-02-02" }, { "version": "0.1.2", "date": "2026-02-26" }, { "version": "0.1.3", "date": "2026-03-10" }, { "version": "0.1.4", "date": "2026-04-08" }, { "version": "0.1.5", "date": "2026-06-16" }, { "version": "0.2.0", "date": "2026-07-02" } ], "_exports": [ "aggregate_enrichment", "aggregate_omics", "bayes_enrich", "bayes_summary", "classify_omics_pattern", "collapse_multilayer_scores", "EXTID2NAME", "extract_mnsea_subnetwork", "geneID", "geneInCategory", "get_mnsea_contribution", "get_omics_contribution", "gsea", "gsea_gson", "gseaScores", "gsfilter", "harmonize_ids", "mnsea", "mnsea_gson", "nsea", "nsea_gson", "ora", "ora_gson", "prepare_multilayer_network", "prepare_network", "propagate_multilayer", "select_features_for_ora", "setReadable", "show", "summary" ], "_help": [ { "page": "aggregate_enrichment", "title": "Aggregate multiple enrichment results (Late Fusion)", "topics": [ "aggregate_enrichment" ] }, { "page": "aggregate_omics", "title": "Aggregate multi-omics gene/protein-level statistics", "topics": [ "aggregate_omics" ] }, { "page": "bayes_enrich", "title": "Bayesian term selection for enrichment results", "topics": [ "bayes_enrich" ] }, { "page": "bayes_summary", "title": "Summarize Bayesian enrichment results", "topics": [ "bayes_summary" ] }, { "page": "classify_omics_pattern", "title": "Classify pathway-level multi-omics patterns", "topics": [ "classify_omics_pattern" ] }, { "page": "collapse_multilayer_scores", "title": "Collapse multi-layer diffusion scores", "topics": [ "collapse_multilayer_scores" ] }, { "page": "compareClusterResult-class", "title": "Class \"compareClusterResult\" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.", "topics": [ "compareClusterResult-class", "plot,compareClusterResult-method", "show,compareClusterResult-method", "summary,compareClusterResult-method" ] }, { "page": "enrichit_params", "title": "Common parameters for enrichit functions", "topics": [ "enrichit_params" ] }, { "page": "enrichResult-class", "title": "Class \"enrichResult\" This class represents the result of enrichment analysis.", "topics": [ "enrichResult-class", "show,enrichResult-method", "summary,enrichResult-method" ] }, { "page": "EXTID2NAME", "title": "EXTID2NAME", "topics": [ "EXTID2NAME" ] }, { "page": "extract_mnsea_subnetwork", "title": "Extract pathway subnetwork data from a 'mnseaResult'", "topics": [ "extract_mnsea_subnetwork" ] }, { "page": "geneID", "title": "geneID generic", "topics": [ "geneID" ] }, { "page": "geneInCategory", "title": "geneInCategory generic", "topics": [ "geneInCategory" ] }, { "page": "get_mnsea_contribution", "title": "Get cached contribution tables from a 'mnseaResult'", "topics": [ "get_mnsea_contribution" ] }, { "page": "get_omics_contribution", "title": "Get gene-level omics contribution for a specific pathway", "topics": [ "get_omics_contribution" ] }, { "page": "gsea", "title": "Gene Set Enrichment Analysis (GSEA)", "topics": [ "gsea" ] }, { "page": "gsea_gson", "title": "gsea_gson", "topics": [ "gsea_gson" ] }, { "page": "gseaResult-class", "title": "Class \"gseaResult\" This class represents the result of GSEA analysis", "topics": [ "gseahResult-class", "gseaResult-class", "show,gseaResult-method", "summary,gseaResult-method" ] }, { "page": "gseaScores", "title": "Calculate GSEA Running Enrichment Scores", "topics": [ "gseaScores" ] }, { "page": "gsfilter", "title": "gsfilter", "topics": [ "gsfilter" ] }, { "page": "harmonize_ids", "title": "Harmonize feature IDs to a target space", "topics": [ "harmonize_ids" ] }, { "page": "mnsea", "title": "Multi-layer Network-based Gene Set Enrichment Analysis", "topics": [ "mnsea" ] }, { "page": "mnsea_gson", "title": "Multi-layer NSEA using a GSON object", "topics": [ "mnsea_gson" ] }, { "page": "mnseaResult-class", "title": "Class \"mnseaResult\" This class represents the result of multi-layer Network-based Set Enrichment Analysis.", "topics": [ "mnseaResult-class" ] }, { "page": "nsea", "title": "Network-based Gene Set Enrichment Analysis", "topics": [ "nsea" ] }, { "page": "nsea_gson", "title": "Network-based GSEA using a GSON object", "topics": [ "nsea_gson" ] }, { "page": "nseaResult-class", "title": "Class \"nseaResult\" This class represents the result of Network-based Set Enrichment Analysis (NSEA).", "topics": [ "nseaResult-class" ] }, { "page": "ora", "title": "Over-Representation Analysis (ORA)", "topics": [ "ora" ] }, { "page": "ora_gson", "title": "ora-gson", "topics": [ "ora_gson" ] }, { "page": "prepare_multilayer_network", "title": "Prepare multi-layer network for repeated propagation", "topics": [ "prepare_multilayer_network" ] }, { "page": "prepare_network", "title": "Prepare network for repeated NSEA runs", "topics": [ "prepare_network" ] }, { "page": "propagate_multilayer", "title": "Propagate signals on a multi-layer network", "topics": [ "propagate_multilayer" ] }, { "page": "select_features_for_ora", "title": "Select features for ORA", "topics": [ "select_features_for_ora" ] }, { "page": "setReadable", "title": "setReadable", "topics": [ "setReadable" ] }, { "page": "show-methods", "title": "show method", "topics": [ "show", "show,mnseaResult-method", "show,nseaResult-method" ] }, { "page": "summary-methods", "title": "summary method", "topics": [ "summary" ] } ], "_readme": "https://github.com/cran/enrichit/raw/HEAD/README.md", "_rundeps": [ "cli", "digest", "fs", "lattice", "Matrix", "rappdirs", "Rcpp", "RcppEigen", "rlang", "yulab.utils" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 6.538930692493127, "_indexed": false, "_nocasepkg": "enrichit", "_universes": [ "cran" ], "_indexurl": "https://guangchuangyu.r-universe.dev/enrichit", "_previous": "0.1.5", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.0", "date": "2026-07-02T21:30:23.000Z", "distro": "resolute", "arch": "aarch64", "commit": "fb787911b606956438ea0245139709d1adc5214d", "fileid": "https://r2.ropensci.org/517babd54a72221ddadd5ccb0c7f649e6a08e919cf7c2dcf1e107c39c6fb23db", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/28622371279" }, { "r": "4.7.0", "os": "linux", "version": "0.2.0", "date": "2026-07-02T21:29:47.000Z", "distro": "resolute", "arch": "x86_64", "commit": "fb787911b606956438ea0245139709d1adc5214d", "fileid": "https://r2.ropensci.org/dd934929e0bbebcc38b55bd3799d6be20f41000edd0c450b6e2885e335fb6a00", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/28622371279" }, { "r": "4.6.1", "os": "linux", "version": "0.2.0", "date": "2026-07-02T21:29:38.000Z", "distro": "resolute", "arch": "aarch64", "commit": "fb787911b606956438ea0245139709d1adc5214d", "fileid": "https://r2.ropensci.org/63a0936a46192afe03a55ed160098062a46861942b67ab1e865dbfd3cc29ac73", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/28622371279" }, { "r": "4.6.1", "os": "linux", "version": "0.2.0", "date": "2026-07-02T21:30:37.000Z", "distro": "resolute", "arch": "x86_64", "commit": "fb787911b606956438ea0245139709d1adc5214d", "fileid": "https://r2.ropensci.org/ec8e8e8c2c6581e2defaddf01fc5b4a713e5782e3de75d817d4e5e8d10c8b413", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/28622371279" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.0", "date": "2026-07-02T21:30:27.000Z", "arch": "emscripten", "commit": "fb787911b606956438ea0245139709d1adc5214d", "fileid": "https://r2.ropensci.org/13127a3e383a4a12dcd321a8641842ca4819cad05c3ccf2e836de62dd7924d44", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/28622371279" } ] }