Package: CBEA 1.5.0

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:Quang Nguyen [aut, cre]

CBEA_1.5.0.tar.gz
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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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

hmp_gingival - Gingival data set from the Human Microbiome Project

On BioConductor:CBEA-1.5.0(bioc 3.20)CBEA-1.4.0(bioc 3.19)

bioconductor-package

10 exports 0.36 score 123 dependencies

Last updated 2 months agofrom:0234eb6881

Exports:cbea dlst dmnorm get_raw_score glance gmean gmeanRow plst pmnorm tidy

Dependencies:abind AnnotationDbi ape askpass base64enc BH Biobase BiocGenerics BiocIO BiocParallel BiocSet Biostrings bit bit64 blob bslib cachem cli codetools colorspace cpp11 crayon crosstalk curl data.table DBI DelayedArray digest dplyr evaluate fansi farver fastmap fitdistrplus fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue goftest gtable highr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite KEGGREST kernlab knitr labeling lambda.r later lattice lazyeval lifecycle lmom magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime mixtools munsell nlme ontologyIndex openssl pillar pkgconfig plogr plotly plyr png promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown RSQLite S4Arrays S4Vectors sass scales segmented SingleCellExperiment snow SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tidytree tinytex treeio TreeSummarizedExperiment UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml yulab.utils zlibbioc

CBEA: Competitive Balances for Taxonomic Enrichment Analysis

Quang P.Nguyen, Anne G. Hoen, H. Robert Frost

Rendered frombasic_usage.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2022-03-24
Started: 2021-06-08

Citation

Development and contributors

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