Package Recipe 'bioconductor-legato'

recipe bioconductor-legato

LegATo: Longitudinal mEtaGenomic Analysis Toolkit

Homepage:: https://bioconductor.org/packages/3.22/data/experiment/html/LegATo.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-legato/meta.yaml

LegATo is a suite of open-source software tools for longitudinal microbiome analysis. It is extendable to several different study forms with optimal ease-of-use for researchers. Microbiome time-series data presents distinct challenges including complex covariate dependencies and variety of longitudinal study designs. This toolkit will allow researchers to determine which microbial taxa are affected over time by perturbations such as onset of disease or lifestyle choices, and to predict the effects of these perturbations over time, including changes in composition or stability of commensal bacteria.

package bioconductor-legato¶

Versions:

1.4.0-0

Depends:

on bioconductor-animalcules >=1.26.0,<1.27.0
on bioconductor-data-packages >=20260207
on bioconductor-multiassayexperiment >=1.36.0,<1.37.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on curl
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-dplyr
on r-ggplot2
on r-magrittr
on r-plyr
on r-rlang
on r-stringr
on r-tibble
on r-tidyr
on r-tidyselect

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-legato

to add into an existing workspace instead, run:

pixi add bioconductor-legato

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-legato

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-legato

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-legato:<tag>

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