recipe maaslin3

"Refining and extending generalized multivariate linear models for meta-omic association discovery"

Homepage:

https://github.com/biobakery/maaslin3

License:

Custom

Recipe:

/maaslin3/meta.yaml

MaAsLin 3 refines and extends generalized multivariate linear models for meta-omicron association discovery. It finds abundance and prevalence associations between microbiome meta-omics features and complex metadata in population-scale epidemiological studies. The software includes multiple analysis methods (including support for multiple covariates, repeated measures, and ordered predictors), filtering, normalization, and transform options to customize analysis for your specific study.

package maaslin3

versions:

0.99.16-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-treesummarizedexperiment:

>=2.14.0,<2.15.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-ggnewscale:

depends r-ggplot2:

depends r-lme4:

depends r-lmertest:

depends r-logging:

depends r-multcomp:

depends r-optparse:

depends r-patchwork:

depends r-pbapply:

depends r-plyr:

depends r-rcolorbrewer:

depends r-rlang:

depends r-scales:

depends r-survival:

depends r-tibble:

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 maaslin3

and update with::

   mamba update maaslin3

To create a new environment, run:

mamba create --name myenvname maaslin3

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/maaslin3:<tag>

(see `maaslin3/tags`_ for valid values for ``<tag>``)

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