recipe bioconductor-mbecs

Evaluation and correction of batch effects in microbiome data-sets






The Microbiome Batch Effect Correction Suite (MBECS) provides a set of functions to evaluate and mitigate unwated noise due to processing in batches. To that end it incorporates a host of batch correcting algorithms (BECA) from various packages. In addition it offers a correction and reporting pipeline that provides a preliminary look at the characteristics of a data-set before and after correcting for batch effects.

package bioconductor-mbecs

(downloads) docker_bioconductor-mbecs



depends bioconductor-limma:


depends bioconductor-phyloseq:


depends bioconductor-sva:


depends r-base:


depends r-cluster:

depends r-dplyr:

depends r-ggplot2:

depends r-gridextra:

depends r-lme4:

depends r-lmertest:

depends r-magrittr:

depends r-matrix:

depends r-pheatmap:

depends r-rmarkdown:

depends r-ruv:

depends r-tibble:

depends r-tidyr:

depends r-vegan:



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-mbecs

and update with::

   mamba update bioconductor-mbecs

To create a new environment, run:

mamba create --name myenvname bioconductor-mbecs

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-mbecs/tags`_ for valid values for ``<tag>``)

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