{ "_id": "6adfe3fd4d02104fb3ebfd29", "Package": "TaxSEA", "Type": "Package", "Title": "Taxon Set Enrichment Analysis", "Version": "1.5.8", "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 makes metagenomic data easier to interpret. Rather\nthan reading species one at a time, it tests whether a-priori\ndefined sets of taxa shift together, drawing on public\ndatabases (BugSigDB, MiMeDB, GutMGene, mBodyMap, BacDive and\nGMRepoV2) and on sets collated from the literature. Two\napproaches are provided. TaxSEA takes taxon names or NCBI IDs\nwith a rank per taxon, such as a fold change or correlation\ncoefficient, and tests each set with a Kolmogorov-Smirnov test.\nssTaxSEA scores every set in a single sample as the mean\ncentered log-ratio of its members, giving a per-sample value to\nuse in any downstream model. Both work with any taxonomic\nprofiling technology, including 16S rRNA gene sequencing,\nshotgun metagenomics and metatranscriptomics.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "false", "VignetteBuilder": "knitr", "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", "Config/roxygen2/version": "8.1.0", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-10-26 06:37:55 UTC", "RemoteUrl": "https://github.com/bioc/TaxSEA", "RemoteRef": "HEAD", "RemoteSha": "9831356494cf3096773098dea7216393db07dffb", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-26 23:27:41 UTC", "User": "root" }, "Author": "Feargal Ryan [aut, cre, fnd] (ORCID:\n, funding: Supported by\nNHMRC Investigator Grant)", "Maintainer": "Feargal Ryan ", "_user": "bioc", "_type": "src", "_file": "TaxSEA_1.5.8.tar.gz", "_fileid": "https://r2.ropensci.org/ba4392d768210598e51c85b74f329d81bee4ff8557803c20beefbcbd0263d973", "_filesize": 2319636, "_sha256": "ba4392d768210598e51c85b74f329d81bee4ff8557803c20beefbcbd0263d973", "_expires": "2027-02-03T23:36:27.000Z", "_created": "2026-10-26T23:27:41.000Z", "_published": "2026-10-26T23:36:29.628Z", "_upstream": "https://github.com/bioc/TaxSEA", "_status": "success", "_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 }, "_jobs": [ { "job": 121911578752, "time": 223, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "12697198326" }, { "job": 121911578804, "time": 296, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12696892857" }, { "job": 121911578849, "time": 308, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12697787499" }, { "job": 121911578932, "time": 153, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12696323552" }, { "job": 121911578924, "time": 168, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12697907316" }, { "job": 121909492246, "time": 322, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12697836645" }, { "job": 121911578862, "time": 120, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12697677277" }, { "job": 121911578833, "time": 173, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12697283012" }, { "job": 121911578805, "time": 107, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12696492646" }, { "job": 121911578869, "time": 131, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12697048050" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/40419288023", "_commit": { "id": "9831356494cf3096773098dea7216393db07dffb", "author": "feargalr ", "committer": "feargalr ", "message": "ssTaxSEA(): add a top-k reference and a proportion scale (v1.5.8)\n\nThe standard CLR centers each sample on the mean log value of every\ntaxon, zeros included. When many rare taxa drop out, as after\nchemotherapy, that reference falls and every surviving taxon's score\nrises, so hundreds of overlapping sets increase together with no change\namong the survivors. Adjusting for richness downstream does not remove\nit, and the reference also moves whenever rows are filtered differently.\n\nreference = \"top_k\" centers each sample on its top_k (default 20) most\nabundant detected taxa instead, capped at the number detected so zeros\nnever enter it. Rare taxa are still scored but no longer move everyone\nelse's score. K = 20 had the best worst case when known perturbations\n(rare-taxon loss, a bloom, losing the dominant taxon, lower depth) were\napplied to 2,071 curatedMetagenomicData samples across 85 studies.\n\nscale = \"proportion\" divides each sample by its total and applies the\npseudocount as a proportion (default 1e-6), so counts, proportions and\npercentages give the same scores and the pseudocount does not vary with\ndepth.\n\nPercentages were previously accepted on the count scale, where the 0.5\npseudocount (half a percent) swamped every rarer taxon. They are now\nrefused with a pointer to scale = \"proportion\". Defaults are unchanged.\n\nCo-Authored-By: Claude Opus 5.5 \n", "time": 1792996675 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "S4Vectors", "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": "2025-44", "n": 2 }, { "week": "2026-03", "n": 20 }, { "week": "2026-07", "n": 6 }, { "week": "2026-38", "n": 9 }, { "week": "2026-39", "n": 2 }, { "week": "2026-44", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.5.7", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.4.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "microbiome", "metagenomics", "sequencing", "genesetenrichment", "rnaseq" ], "_stars": 12, "_contributors": [ { "user": "feargalr", "count": 195, "uuid": 7561275 }, { "user": "jwokaty", "count": 6, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 479, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 322, "source": "https://www.bioconductor.org/packages/stats/bioc/TaxSEA" }, "_devurl": "https://github.com/feargalr/taxsea", "_pkgdown": "https://feargalr.github.io/TaxSEA/", "_searchresults": 14, "_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/readme.html", "extra/readme.md", "extra/TaxSEA.html" ], "_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", "Usage", "From a count matrix", "A single sample", "With the built-in database", "From a TreeSummarizedExperiment", "Interpreting the scores", "Practical considerations", "When to use ssTaxSEA vs TaxSEA", "Downstream analysis" ], "created": "2026-02-12 03:27:48", "modified": "2026-10-26 06:37:55", "commits": 3 }, { "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 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