recipe bioconductor-phyloseq

Handling and analysis of high-throughput microbiome census data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/phyloseq.html

License:

AGPL-3

Recipe:

/bioconductor-phyloseq/meta.yaml

Links:

biotools: phyloseq

phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.

package bioconductor-phyloseq

versions:

1.46.0-0,  1.44.0-0,  1.42.0-0,  1.38.0-0,  1.36.0-0,  1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-0, 

1.46.0-0,  1.44.0-0,  1.42.0-0,  1.38.0-0,  1.36.0-0,  1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.26.1-0,  1.26.0-0,  1.24.2-0,  1.22.3-0,  1.20.0-1,  1.20.0-0,  1.19.1-0,  1.16.2-1,  1.14.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biomformat:

>=1.30.0,<1.31.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-multtest:

>=2.58.0,<2.59.0

depends r-ade4:

>=1.7-4

depends r-ape:

>=5.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cluster:

>=2.0.4

depends r-data.table:

>=1.10.4

depends r-foreach:

>=1.4.3

depends r-ggplot2:

>=2.1.0

depends r-igraph:

>=1.0.1

depends r-plyr:

>=1.8.3

depends r-reshape2:

>=1.4.1

depends r-scales:

>=0.4.0

depends r-vegan:

>=2.5

requirements:

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-phyloseq

and update with::

   mamba update bioconductor-phyloseq

To create a new environment, run:

mamba create --name myenvname bioconductor-phyloseq

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-phyloseq:<tag>

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

Download stats

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