CBEA

DOI: 10.18129/B9.bioc.CBEA    

Competitive Balances for Taxonomic Enrichment Analysis in R

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	Basic Usage
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, GeneSetEnrichment, Metagenomics, Microbiome, Software
Version	1.0.0
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 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
LinkingTo	Rcpp
Suggests	phyloseq, BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyverse, roxygen2, mia, purrr
SystemRequirements
Enhances
URL	https://github.com/qpmnguyen/CBEA https://qpmnguyen.github.io/CBEA/
BugReports	https://github.com/qpmnguyen/CBEA//issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CBEA_1.0.0.tar.gz
Windows Binary	CBEA_1.0.0.zip (64-bit only)
macOS Binary (x86_64)	CBEA_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CBEA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CBEA
Package Short Url	https://bioconductor.org/packages/CBEA/
Package Downloads Report	Download Stats