recipe bioconductor-cbea

Competitive Balances for Taxonomic Enrichment Analysis in R

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-cbea/meta.yaml

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

versions:

1.3.0-0,  1.2.0-2,  1.2.0-1,  1.2.0-0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-biocset:

>=1.14.0,<1.15.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends bioconductor-treesummarizedexperiment:

>=2.8.0,<2.9.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

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:

>=1.0.7

depends r-rlang:

depends r-tibble:

depends r-tidyr:

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

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

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Link to this page

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