Package Recipe 'bioconductor-microstasis'

recipe bioconductor-microstasis

Microbiota STability ASsessment via Iterative cluStering

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/microSTASIS.html
License:: GPL-3
Recipe:: /bioconductor-microstasis/meta.yaml

The toolkit 'µSTASIS', or microSTASIS, has been developed for the stability analysis of microbiota in a temporal framework by leveraging on iterative clustering. Concretely, the core function uses Hartigan-Wong k-means algorithm as many times as possible for stressing out paired samples from the same individuals to test if they remain together for multiple numbers of clusters over a whole data set of individuals. Moreover, the package includes multiple functions to subset samples from paired times, validate the results or visualize the output.

package bioconductor-microstasis¶

Versions:

1.6.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-biocparallel >=1.40.0,<1.41.0
on bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0
on r-base >=4.4,<4.5.0a0
on r-ggplot2
on r-ggside
on r-rlang
on r-stringr

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-microstasis

to add into an existing workspace instead, run:

pixi add bioconductor-microstasis

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-microstasis

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-microstasis

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-microstasis:<tag>

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