{ "_id": "6a1af15f1d7bb097a09f701e", "Package": "TaxSEA", "Type": "Package", "Title": "Taxon Set Enrichment Analysis", "Version": "1.5.0", "Authors@R": "c(person(\"Feargal\", \"Ryan\", \nemail = \"feargalr@gmail.com\",\nrole = c(\"aut\", \"cre\",\"fnd\"),comment = c(ORCID = \"0000-0002-1565-4598\",\nfunding = \"Supported by NHMRC Investigator Grant\")))", "Description": "TaxSEA is an R package for Taxon Set Enrichment Analysis,\nwhich utilises a Kolmogorov-Smirnov test analyses to\ninvestigate differential abundance analysis output for whether\nthere are alternations in a-priori defined sets of taxa from\npublic databases (BugSigDB, MiMeDB, GutMGene, mBodyMap, BacDive\nand GMRepoV2) and collated from the literature. TaxSEA takes as\ninput a list of taxonomic identifiers (e.g. species names, NCBI\nIDs etc.) and a rank (E.g. fold change, correlation\ncoefficient). TaxSEA be applied to any microbiota taxonomic\nprofiling technology (array-based, 16S rRNA gene sequencing,\nshotgun metagenomics & metatranscriptomics etc.) and enables\nresearchers to rapidly contextualize their findings within the\nbroader literature to accelerate interpretation of results.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "false", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "biocViews": "Microbiome, Metagenomics, Sequencing, GeneSetEnrichment,\nRNASeq", "URL": "https://github.com/feargalr/taxsea,\nhttps://feargalr.github.io/TaxSEA/", "BugReports": "https://github.com/feargalr/taxsea/issues", "Config/testthat/edition": "3", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:05:02 UTC", "RemoteUrl": "https://github.com/bioc/TaxSEA", "RemoteRef": "HEAD", "RemoteSha": "ae582a26297f236feb1584848c75994be24b3a84", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:44:00 UTC", "User": "root" }, "Author": "Feargal Ryan [aut, cre, fnd] (ORCID:\n, funding: Supported by\nNHMRC Investigator Grant)", "Maintainer": "Feargal Ryan ", "MD5sum": "03cd1f5694fe5d039b4b93e466b2a7af", "_user": "bioc", "_type": "src", "_file": "TaxSEA_1.5.0.tar.gz", "_fileid": "2b3b5d57f21912899ddb119069f7d6e896d5a3a4f0f749a07acdf6b48d684efc", "_filesize": 1808793, "_sha256": "2b3b5d57f21912899ddb119069f7d6e896d5a3a4f0f749a07acdf6b48d684efc", "_created": "2026-05-30T09:44:00.000Z", "_published": "2026-05-30T14:17:03.119Z", "_jobs": [ { "job": 78640456953, "time": 189, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307434203" }, { "job": 78640456954, "time": 229, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307437834" }, { "job": 78640456955, "time": 257, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7307440291" }, { "job": 78640456960, "time": 236, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7308800867" }, { "job": 78640456958, "time": 134, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7308788977" }, { "job": 78639785068, "time": 203, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307270533" }, { "job": 78640456957, "time": 152, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307430606" }, { "job": 78640456965, "time": 145, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7307429853" }, { "job": 78640456963, "time": 156, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7307430918" }, { "job": 78640456962, "time": 132, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7307428674" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676676820", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/TaxSEA", "_commit": { "id": "ae582a26297f236feb1584848c75994be24b3a84", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381502 }, "_maintainer": { "name": "Feargal Ryan", "email": "feargalr@gmail.com", "login": "feargalr", "bluesky": "@feargalr.bsky.social", "linkedin": "in/feargal-ryan-978a75135", "orcid": "0000-0002-1565-4598", "description": "", "uuid": 7561275 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "bugsigdbr", "role": "Suggests" }, { "package": "fgsea", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "mia", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-24", "n": 1 }, { "week": "2025-29", "n": 4 }, { "week": "2025-30", "n": 1 }, { "week": "2025-32", "n": 3 }, { "week": "2025-33", "n": 2 }, { "week": "2025-34", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-03", "n": 20 }, { "week": "2026-07", "n": 6 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.5.0", "bioc": "3.24" }, { "branch": "release", "version": "1.4.0", "bioc": "3.23" } ], "_topics": [ "microbiome", "metagenomics", "sequencing", "genesetenrichment", "rnaseq" ], "_stars": 10, "_contributors": [ { "user": "feargalr", "count": 183, "uuid": 7561275 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 246, "source": "https://www.bioconductor.org/packages/stats/bioc/TaxSEA" }, "_devurl": "https://github.com/feargalr/taxsea", "_pkgdown": "https://feargalr.github.io/TaxSEA/", "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/TaxSEA.html", "manual.pdf" ], "_homeurl": "https://github.com/feargalr/taxsea", "_realowner": "bioc", "_cranurl": false, "_exports": [ "get_ncbi_taxon_ids", "get_taxon_sets", "ssTaxSEA", "taxon_rank_sets", "TaxSEA" ], "_datasets": [ { "name": "NCBI_ids", "title": "NCBI IDs Dataset", "object": "NCBI_ids", "file": "NCBI_ids.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "TaxSEA_db", "title": "TaxSEA Database A dataset containing taxon sets. Each item in the list is a taxon set, and each member within a taxon set is a taxon.", "object": "TaxSEA_db", "file": "TaxSEA_db.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "TaxSEA_test_data", "title": "TaxSEA Test Data", "object": "TaxSEA_test_data", "file": "TaxSEA_test_data.rda", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "get_ncbi_taxon_ids", "title": "Retrieve NCBI Taxonomy IDs for a list of taxon names", "topics": [ "get_ncbi_taxon_ids" ] }, { "page": "get_taxon_sets", "title": "Retrieve Taxon Sets from TaxSEA Library", "topics": [ "get_taxon_sets" ] }, { "page": "NCBI_ids", "title": "NCBI IDs Dataset", "topics": [ "NCBI_ids" ] }, { "page": "ssTaxSEA", "title": "Single-Sample Taxon Set Enrichment Analysis", "topics": [ "ssTaxSEA" ] }, { "page": "taxon_rank_sets", "title": "Taxon Rank Set Enrichment Analysis", "topics": [ "taxon_rank_sets" ] }, { "page": "TaxSEA", "title": "TaxSEA: Taxon Set Enrichment Analysis", "topics": [ "TaxSEA" ] }, { "page": "TaxSEA_db", "title": "TaxSEA Database A dataset containing taxon sets. Each item in the list is a taxon set, and each member within a taxon set is a taxon.", "topics": [ "TaxSEA_db" ] }, { "page": "TaxSEA_test_data", "title": "TaxSEA Test Data", "topics": [ "TaxSEA_test_data" ] } ], "_readme": "https://github.com/bioc/TaxSEA/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "ORA_vs_ES.Rmd", "filename": "ORA_vs_ES.html", "title": "Analysis types", "engine": "knitr::rmarkdown", "headings": [ "ORA vs Enrichment (two ways to run TaxSEA)", "Enrichment (rank-based)", "What it does (in plain terms)", "When to use it (recommended in most cases)", "Pros", "Cons", "ORA (Over-Representation Analysis)", "When to use it", "Recommended practice" ], "created": "2026-01-14 05:20:20", "modified": "2026-01-14 05:20:20", "commits": 1 }, { "source": "FAQs.Rmd", "filename": "FAQs.html", "title": "Frequently Asked Questions", "engine": "knitr::rmarkdown", "headings": [ "What problem does TaxSEA actually solve?", "Is TaxSEA a replacement for differential abundance?", "Can I use TaxSEA even when there are no individual species level differences?", "How is this different from functional profiling tools like HUMAnN3?", "Does this only work for the human gut microbiome?", "Do I need differential abundance results first?", "Why use ranks instead of thresholds?", "Isn’t this just gene set enrichment, but for microbes?", "Will this work if my DA results are messy or inconsistent?", "Have you shown TaxSEA is accurate?", "When should I not use TaxSEA?", "Can I use TaxSEA with 16S rRNA gene sequencing data?", "Why does TaxSEA use species-level data instead of strain-level?" ], "created": "2026-01-13 05:45:35", "modified": "2026-01-13 05:45:35", "commits": 1 }, { "source": "single-sample-enrichment.Rmd", "filename": "single-sample-enrichment.html", "title": "Single-sample enrichment with ssTaxSEA", "engine": "knitr::rmarkdown", "headings": [ "Why per-person enrichment?", "How it works", "Why z-scoring matters", "When to use ssTaxSEA vs TaxSEA", "Usage", "From a count matrix", "From a TreeSummarizedExperiment", "With custom taxon sets", "Interpreting the output", "Practical considerations" ], "created": "2026-02-12 00:34:21", "modified": "2026-02-12 00:34:21", "commits": 1 }, { "source": "Taxonomic-aggregation.Rmd", "filename": "Taxonomic-aggregation.html", "title": "Testing higher taxonomic levels without collapsing your data", "engine": "knitr::rmarkdown", "headings": [], "created": "2026-01-13 06:14:45", "modified": "2026-02-10 01:10:25", "commits": 3 }, { "source": "TaxSEA.Rmd", "filename": "TaxSEA.html", "title": "TaxSEA", "author": "Feargal Ryan", "engine": "knitr::rmarkdown", "headings": [ "TaxSEA: Taxon Set Enrichment Analysis", "Installation", "Taxon set database", "Test data", "Functions", "Usage", "Retrieve sets containing a particular taxon", "Running an enrichment analysis", "Run TaxSEA with test data", "Output", "BugSigDB", "TaxSEA database with other enrichment tools" ], "created": "2024-12-09 00:37:46", "modified": "2025-04-06 03:38:56", "commits": 4 }, { "source": "why-taxon-set-enrichment.Rmd", "filename": "why-taxon-set-enrichment.html", "title": "Why use taxon set enrichment analysis?", "engine": "knitr::rmarkdown", "headings": [ "The challenge with interpreting differences in microbiome data", "The idea behind Taxon Set Enrichment Analysis", "But isn’t this what functional profiling tools (e.g. HUMAnN3) do?" ], "created": "2026-01-13 05:45:35", "modified": "2026-01-15 00:20:27", "commits": 2 } ], "_score": 6.477121254719663, "_indexed": true, "_nocasepkg": "taxsea", "_universes": [ "bioc", "feargalr" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.5.0", "date": "2026-05-30T10:13:01.000Z", "distro": "noble", "commit": "ae582a26297f236feb1584848c75994be24b3a84", "fileid": "6e7a9e4d3fabd0e2c829bd71bfae5edd6b7d1254085b1604cc050e373f53dd99", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676676820" }, { "r": "4.6.0", "os": "linux", "version": "1.5.0", "date": "2026-05-30T10:13:26.000Z", "distro": "noble", "commit": "ae582a26297f236feb1584848c75994be24b3a84", "fileid": "61ebb530d95e2561763e3912a3dd089ba159328e3ab67eca403acd95bfa4c94e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676676820" }, { "r": "4.5.3", "os": "mac", "version": "1.5.0", "date": "2026-05-30T14:16:29.000Z", "commit": "ae582a26297f236feb1584848c75994be24b3a84", "fileid": "cd8e6ab5ad805180e88599f08a50e2c6653ec6719b79df2fa6feb8be89439cef", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676676820" }, { "r": "4.6.0", "os": "mac", "version": "1.5.0", "date": "2026-05-30T14:14:11.000Z", "commit": "ae582a26297f236feb1584848c75994be24b3a84", "fileid": "d47f51fbbfd328880d25315445a3537ed702bff26c55c85d4eb459679c4d8255", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676676820" }, { "r": "4.6.0", "os": "wasm", "version": "1.5.0", "date": "2026-05-30T10:12:25.000Z", "commit": "ae582a26297f236feb1584848c75994be24b3a84", "fileid": "5ac4ea87c5fcb3cb486b81f1e0a2208a7944fa2f25fb581e99d48c64fe97c12b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676676820" }, { "r": "4.7.0", "os": "win", "version": "1.5.0", "date": "2026-05-30T10:11:31.000Z", "commit": "ae582a26297f236feb1584848c75994be24b3a84", "fileid": "4583e168758e98104c3dddd7eb6beb246f80dfc890e55702c2573dff3d5f8b4d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676676820" }, { "r": "4.5.3", "os": "win", "version": "1.5.0", "date": "2026-05-30T10:11:36.000Z", "commit": "ae582a26297f236feb1584848c75994be24b3a84", "fileid": "6eb73bb12b8312bc4f253889242d7146dd8eb1a35fdd2a9e987be28f2ba86370", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676676820" }, { "r": "4.6.0", "os": "win", "version": "1.5.0", "date": "2026-05-30T10:11:14.000Z", "commit": "ae582a26297f236feb1584848c75994be24b3a84", "fileid": "990bb2e9b90cfe2e1f861f417e2d4b0611cc0e6c02bdcf1a5abb8a64b21b69f0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676676820" } ] }