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CBEA

This is the development version of CBEA; for the stable release version, see CBEA.

Competitive Balances for Taxonomic Enrichment Analysis in R


Bioconductor version: Development (3.19)

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.

Author: Quang Nguyen [aut, cre]

Maintainer: Quang Nguyen <quangpmnguyen at gmail.com>

Citation (from within R, enter citation("CBEA")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CBEA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CBEA")
Basic Usage HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DataImport, GeneSetEnrichment, Metagenomics, Microbiome, Software
Version 1.3.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License MIT + file LICENSE
Depends R (>= 4.2.0)
Imports BiocParallel, BiocSet, dplyr, lmom, fitdistrplus, magrittr, methods, mixtools, Rcpp (>= 1.0.7), stats, SummarizedExperiment, tibble, TreeSummarizedExperiment, tidyr, glue, generics, rlang, goftest
System Requirements
URL https://github.com/qpmnguyen/CBEA https://qpmnguyen.github.io/CBEA/
Bug Reports https://github.com/qpmnguyen/CBEA//issues
See More
Suggests phyloseq, BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyverse, roxygen2, mia, purrr
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CBEA_1.3.0.tar.gz
Windows Binary CBEA_1.3.0.zip
macOS Binary (x86_64) CBEA_1.3.0.tgz
macOS Binary (arm64) CBEA_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CBEA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CBEA
Bioc Package Browser https://code.bioconductor.org/browse/CBEA/
Package Short Url https://bioconductor.org/packages/CBEA/
Package Downloads Report Download Stats