Package Recipe 'bioconductor-microbiotaprocess'

recipe bioconductor-microbiotaprocess

A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/MicrobiotaProcess.html
License:: GPL (>= 3.0)
Recipe:: /bioconductor-microbiotaprocess/meta.yaml

MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It introduces MPSE class, this make it more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy microbiome data structure paradigm and analysis grammar. It provides a wide variety of microbiome data analysis procedures under the unified and common framework (tidy-like framework).

package bioconductor-microbiotaprocess¶

Versions:

1.22.0-0, 1.18.0-0, 1.14.0-0, 1.12.2-0, 1.10.0-0, 1.6.1-0, 1.4.0-0, 1.2.1-0, 1.2.0-0,

1.22.0-0, 1.18.0-0, 1.14.0-0, 1.12.2-0, 1.10.0-0, 1.6.1-0, 1.4.0-0, 1.2.1-0, 1.2.0-0, 1.0.3-0

Depends:

on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-ggtree >=4.0.0,<4.1.0
on bioconductor-ggtreeextra >=1.20.0,<1.21.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-treeio >=1.34.0,<1.35.0
on r-ape
on r-base >=4.5,<4.6.0a0
on r-cli
on r-coin
on r-data.table
on r-dplyr
on r-dtplyr
on r-foreach
on r-ggfun >=0.1.1
on r-ggplot2
on r-ggrepel
on r-ggsignif
on r-ggstar
on r-magrittr
on r-mass
on r-patchwork
on r-pillar
on r-plyr
on r-rlang
on r-tibble
on r-tidyr
on r-tidyselect
on r-tidytree >=0.4.2
on r-vegan
on r-zoo

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-microbiotaprocess

to add into an existing workspace instead, run:

pixi add bioconductor-microbiotaprocess

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-microbiotaprocess

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-microbiotaprocess

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-microbiotaprocess:<tag>

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