recipe bioconductor-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.

package bioconductor-cbea

(downloads) docker_bioconductor-cbea



depends bioconductor-biocparallel:


depends bioconductor-biocset:


depends bioconductor-summarizedexperiment:


depends bioconductor-treesummarizedexperiment:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-base:


depends r-dplyr:

depends r-fitdistrplus:

depends r-generics:

depends r-glue:

depends r-goftest:

depends r-lmom:

depends r-magrittr:

depends r-mixtools:

depends r-rcpp:


depends r-rlang:

depends r-tibble:

depends r-tidyr:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-cbea

and update with::

   mamba update bioconductor-cbea

To create a new environment, run:

mamba create --name myenvname bioconductor-cbea

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-cbea/tags`_ for valid values for ``<tag>``)

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