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/3.18/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:

1.14.0-0,  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 bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-ggtree:

>=3.10.0,<3.11.0

depends bioconductor-ggtreeextra:

>=1.12.0,<1.13.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-treeio:

>=1.26.0,<1.27.0

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-cli:

depends r-coin:

depends r-data.table:

depends r-dplyr:

depends r-dtplyr:

depends r-foreach:

depends r-ggfun:

>=0.1.1

depends r-ggplot2:

depends r-ggrepel:

depends r-ggsignif:

depends r-ggstar:

depends r-magrittr:

depends r-mass:

depends r-patchwork:

depends r-pillar:

depends r-plyr:

depends r-rlang:

depends r-tibble:

depends r-tidyr:

depends r-tidyselect:

depends r-tidytree:

>=0.4.2

depends r-vegan:

depends r-zoo:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-microbiotaprocess

and update with::

   mamba update bioconductor-microbiotaprocess

To create a new environment, run:

mamba create --name myenvname bioconductor-microbiotaprocess

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-microbiotaprocess:<tag>

(see `bioconductor-microbiotaprocess/tags`_ for valid values for ``<tag>``)

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