CBEA
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.21 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CBEA.
Competitive Balances for Taxonomic Enrichment Analysis in R
Bioconductor version: Release (3.21)
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("CBEA")):
Installation
To install this package, start R (version "4.5") 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
| Reference Manual |
Details
| biocViews | DataImport, GeneSetEnrichment, Metagenomics, Microbiome, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (3.5 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 |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |