recipe r-breakaway

Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis. 'breakaway' is the premier package for statistical analysis of microbial diversity. 'breakaway' implements the latest and greatest estimates of species richness, as well as the most commonly used estimates. Methods uniquely available in this package include objective Bayes estimators described in Barger and Bunge (2010) <doi:10.1214/10-BA527>, frequency-ratio-based estimators described in Willis and Bunge (2015) <doi:10.1111/biom.12332>, and as described in Willis, Whitman, and Bunge (2016) <doi:10.1111/rssc.12206>, a linear modeling approach for detecting changes in diversity.

Homepage:

https://adw96.github.io/breakaway/

License:

GPL2 / GPL-2

Recipe:

/r-breakaway/meta.yaml

package r-breakaway

(downloads) docker_r-breakaway

versions:

4.7.9-2,  4.7.9-1,  4.7.9-0,  3.0-0

depends bioconductor-phyloseq:

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-lme4:

depends r-magrittr:

depends r-mass:

depends r-tibble:

requirements:

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 r-breakaway

and update with::

   mamba update r-breakaway

To create a new environment, run:

mamba create --name myenvname r-breakaway

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/r-breakaway:<tag>

(see `r-breakaway/tags`_ for valid values for ``<tag>``)

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Link to this page

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