Package Recipe 'bioconductor-maaslin2'

recipe bioconductor-maaslin2

"Multivariable Association Discovery in Population-scale Meta-omics Studies"

Homepage:: https://bioconductor.org/packages/3.19/bioc/html/Maaslin2.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-maaslin2/meta.yaml

MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. MaAsLin2 is the next generation of MaAsLin.

package bioconductor-maaslin2¶

Versions:

1.18.0-0, 1.16.0-1, 1.16.0-0, 1.14.1-0, 1.12.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-1, 1.4.0-0,

1.18.0-0, 1.16.0-1, 1.16.0-0, 1.14.1-0, 1.12.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-1, 1.4.0-0, 1.0.0-0

Depends:

on bioconductor-edger >=4.0.0,<4.1.0
on bioconductor-metagenomeseq >=1.43.0,<1.44.0
on r-base >=4.3,<4.4.0a0
on r-biglm
on r-car
on r-chemometrics
on r-cplm
on r-data.table
on r-dplyr
on r-ggplot2
on r-glmmtmb
on r-hash
on r-lme4
on r-lmertest
on r-logging
on r-mass
on r-optparse
on r-pbapply
on r-pcapp
on r-pheatmap
on r-pscl
on r-robustbase
on r-tibble
on r-vegan

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-maaslin2

to add into an existing workspace instead, run:

pixi add bioconductor-maaslin2

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-maaslin2

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-maaslin2

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-maaslin2:<tag>

(see bioconductor-maaslin2/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-maaslin2/README.html)