Package: CBEA 1.7.0
Quang Nguyen
CBEA: Competitive Balances for Taxonomic Enrichment Analysis in R
This package implements CBEA, a method to perform set-based analysis for microbiome relative abundance data. This approach constructs a competitive balance between taxa within the set and remainder taxa per sample. More details can be found in the Nguyen et al. 2021+ manuscript. Additionally, this package adds support functions to help users perform taxa-set enrichment analyses using existing gene set analysis methods. In the future we hope to also provide curated knowledge driven taxa sets.
Authors:
CBEA_1.7.0.tar.gz
CBEA_1.7.0.zip(r-4.5)CBEA_1.7.0.zip(r-4.4)CBEA_1.7.0.zip(r-4.3)
CBEA_1.7.0.tgz(r-4.4-x86_64)CBEA_1.7.0.tgz(r-4.4-arm64)CBEA_1.7.0.tgz(r-4.3-x86_64)CBEA_1.7.0.tgz(r-4.3-arm64)
CBEA_1.7.0.tar.gz(r-4.5-noble)CBEA_1.7.0.tar.gz(r-4.4-noble)
CBEA_1.7.0.tgz(r-4.4-emscripten)CBEA_1.7.0.tgz(r-4.3-emscripten)
CBEA.pdf |CBEA.html✨
CBEA/json (API)
NEWS
| # Install 'CBEA' in R: |
| install.packages('CBEA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/qpmnguyen/cbea/issues
Pkgdown site:https://qpmnguyen.github.io
- hmp_gingival - Gingival data set from the Human Microbiome Project
On BioConductor:CBEA-1.7.0(bioc 3.21)CBEA-1.6.0(bioc 3.20)
softwaremicrobiomemetagenomicsgenesetenrichmentdataimportenrichment-analysistaxonomic-enrichment-analysiscpp
Last updated 2 months agofrom:3940bb991b. Checks:OK: 4 NOTE: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win-x86_64 | NOTE | Dec 19 2024 |
| R-4.5-linux-x86_64 | NOTE | Dec 19 2024 |
| R-4.4-win-x86_64 | NOTE | Dec 19 2024 |
| R-4.4-mac-x86_64 | NOTE | Dec 19 2024 |
| R-4.4-mac-aarch64 | NOTE | Dec 19 2024 |
| R-4.3-win-x86_64 | OK | Dec 19 2024 |
| R-4.3-mac-x86_64 | OK | Dec 19 2024 |
| R-4.3-mac-aarch64 | OK | Dec 19 2024 |
Exports:cbeadlstdmnormget_raw_scoreglancegmeangmeanRowplstpmnormtidy
Dependencies:abindAnnotationDbiapeaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiocSetBiostringsbitbit64blobbslibcachemclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdplyrevaluatefansifarverfastmapfitdistrplusfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegoftestgtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTkernlabknitrlabelinglambda.rlaterlatticelazyevallifecyclelmommagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemixtoolsmunsellnlmeontologyIndexopensslpillarpkgconfigplogrplotlyplyrpngpromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownRSQLiteS4ArraysS4VectorssassscalessegmentedSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttidytreetinytextreeioTreeSummarizedExperimentUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlyulab.utilszlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Enrichment analysis using competitive compositional balances (CBEA) | cbea cbea,data.frame-method cbea,matrix-method cbea,TreeSummarizedExperiment-method |
| Get CBEA scores for a given matrix and a vector of column indices | get_raw_score |
| Glance at 'CBEAout' object | glance.CBEAout |
| Geometric mean of a vector | gmean |
| Geometric mean of rows of a matrix | gmeanRow |
| Gingival data set from the Human Microbiome Project | hmp_gingival |
| Creating an output object of type CBEAout | new_CBEAout |
| The Two Component Mixture Normal Distribution | dmnorm pmnorm |
| Print dispatch for CBEAout objects | print.CBEAout |
| Tidy a CBEAout object | tidy.CBEAout |
