recipe bioconductor-mbecs

Evaluation and correction of batch effects in microbiome data-sets

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/MBECS.html

License:

Artistic-2.0

Recipe:

/bioconductor-mbecs/meta.yaml

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

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-phyloseq:

>=1.46.0,<1.47.0

depends bioconductor-sva:

>=3.50.0,<3.51.0

depends r-base:

>=4.3,<4.4.0a0

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:

requirements:

additional platforms:

Installation

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 quay.io/biocontainers/bioconductor-mbecs:<tag>

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

Download stats

Link to this page

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