Package: TaxSEA 1.4.0
Feargal Ryan
TaxSEA: Taxon Set Enrichment Analysis
TaxSEA is an R package for Taxon Set Enrichment Analysis, which utilises a Kolmogorov-Smirnov test analyses to investigate differential abundance analysis output for whether there are alternations in a-priori defined sets of taxa from public databases (BugSigDB, MiMeDB, GutMGene, mBodyMap, BacDive and GMRepoV2) and collated from the literature. TaxSEA takes as input a list of taxonomic identifiers (e.g. species names, NCBI IDs etc.) and a rank (E.g. fold change, correlation coefficient). TaxSEA be applied to any microbiota taxonomic profiling technology (array-based, 16S rRNA gene sequencing, shotgun metagenomics & metatranscriptomics etc.) and enables researchers to rapidly contextualize their findings within the broader literature to accelerate interpretation of results.
Authors:
TaxSEA_1.4.0.tar.gz
TaxSEA_1.4.0.zip(r-4.7)TaxSEA_1.4.0.zip(r-4.6)TaxSEA_1.4.0.zip(r-4.5)
TaxSEA_1.4.0.tgz(r-4.6-any)TaxSEA_1.4.0.tgz(r-4.5-any)
TaxSEA_1.4.0.tar.gz(r-4.7-any)TaxSEA_1.4.0.tar.gz(r-4.6-any)
TaxSEA_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
TaxSEA/json (API)
NEWS
| # Install 'TaxSEA' in R: |
| install.packages('TaxSEA', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/feargalr/taxsea/issues
Pkgdown/docs site:https://feargalr.github.io
- NCBI_ids - NCBI IDs Dataset
- TaxSEA_db - 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.
- TaxSEA_test_data - TaxSEA Test Data
On BioConductor:TaxSEA-1.5.0(bioc 3.24)TaxSEA-1.4.0(bioc 3.23)
microbiomemetagenomicssequencinggenesetenrichmentrnaseq
Last updated from:76ffa276bd (on RELEASE_3_23). Checks:8 WARNING, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 183 | ||
| linux-devel-x86_64 | WARNING | 244 | ||
| source / vignettes | OK | 237 | ||
| linux-release-x86_64 | WARNING | 219 | ||
| macos-release-arm64 | WARNING | 248 | ||
| macos-oldrel-arm64 | WARNING | 99 | ||
| windows-devel | WARNING | 124 | ||
| windows-release | WARNING | 121 | ||
| windows-oldrel | WARNING | 138 | ||
| wasm-release | OK | 148 |
Exports:get_ncbi_taxon_idsget_taxon_setsssTaxSEAtaxon_rank_setsTaxSEA
Dependencies:
Analysis types
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Frequently Asked Questions
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Single-sample enrichment with ssTaxSEA
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Testing higher taxonomic levels without collapsing your data
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Started: 2026-01-13
TaxSEA
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Started: 2024-12-09
Why use taxon set enrichment analysis?
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Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Retrieve NCBI Taxonomy IDs for a list of taxon names | get_ncbi_taxon_ids |
| Retrieve Taxon Sets from TaxSEA Library | get_taxon_sets |
| NCBI IDs Dataset | NCBI_ids |
| Single-Sample Taxon Set Enrichment Analysis | ssTaxSEA |
| Taxon Rank Set Enrichment Analysis | taxon_rank_sets |
| TaxSEA: Taxon Set Enrichment Analysis | TaxSEA |
| 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. | TaxSEA_db |
| TaxSEA Test Data | TaxSEA_test_data |
