Package Recipe 'bioconductor-cbea'

recipe bioconductor-cbea

Competitive Balances for Taxonomic Enrichment Analysis in R

Homepage:: https://bioconductor.org/packages/3.20/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:

1.6.0-0, 1.3.0-0, 1.2.0-2, 1.2.0-1, 1.2.0-0

Depends:

on bioconductor-biocparallel >=1.40.0,<1.41.0
on bioconductor-biocparallel >=1.40.0,<1.41.0a0
on bioconductor-biocset >=1.20.0,<1.21.0
on bioconductor-biocset >=1.20.0,<1.21.0a0
on bioconductor-summarizedexperiment >=1.36.0,<1.37.0
on bioconductor-summarizedexperiment >=1.36.0,<1.37.0a0
on bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0
on bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=13
on liblapack >=3.9.0,<4.0a0
on libstdcxx >=13
on r-base >=4.4,<4.5.0a0
on r-dplyr
on r-fitdistrplus
on r-generics
on r-glue
on r-goftest
on r-lmom
on r-magrittr
on r-mixtools
on r-rcpp >=1.0.7
on r-rlang
on r-tibble
on r-tidyr

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-cbea

to add into an existing workspace instead, run:

pixi add bioconductor-cbea

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-cbea

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cbea

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-cbea/README.html)