Package Recipe 'bioconductor-animalcules'

recipe bioconductor-animalcules

Interactive microbiome analysis toolkit

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/animalcules.html
License:: Artistic-2.0
Recipe:: /bioconductor-animalcules/meta.yaml

animalcules is an R package for utilizing up-to-date data analytics, visualization methods, and machine learning models to provide users an easy-to-use interactive microbiome analysis framework. It can be used as a standalone software package or users can explore their data with the accompanying interactive R Shiny application. Traditional microbiome analysis such as alpha/beta diversity and differential abundance analysis are enhanced, while new methods like biomarker identification are introduced by animalcules. Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.

package bioconductor-animalcules¶

Versions:

1.26.0-0, 1.22.0-0, 1.16.0-0, 1.14.0-0, 1.10.0-0, 1.6.0-1, 1.6.0-0, 1.4.0-0, 1.2.0-0,

1.26.0-0, 1.22.0-0, 1.16.0-0, 1.14.0-0, 1.10.0-0, 1.6.0-1, 1.6.0-0, 1.4.0-0, 1.2.0-0, 1.0.6-0

Depends:

on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-limma >=3.66.0,<3.67.0
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 r-ape
on r-assertthat
on r-base >=4.5,<4.6.0a0
on r-caret
on r-covr
on r-dplyr
on r-dt
on r-forcats
on r-ggforce
on r-ggplot2
on r-gunifrac
on r-lattice
on r-magrittr
on r-matrix
on r-plotly
on r-rentrez
on r-reshape2
on r-rocit
on r-scales
on r-shiny
on r-shinyjs
on r-tibble
on r-tidyr
on r-tsne
on r-umap
on r-vegan
on r-xml

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-animalcules

to add into an existing workspace instead, run:

pixi add bioconductor-animalcules

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-animalcules

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-animalcules

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-animalcules:<tag>

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