recipe bioconductor-philr

Phylogenetic partitioning based ILR transform for metagenomics data

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-philr/meta.yaml

Links:

biotools: philr

PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.

package bioconductor-philr

(downloads) docker_bioconductor-philr

versions:
1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0, 

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.1-0,  1.6.0-0,  1.4.0-0

depends bioconductor-ggtree:

>=3.10.0,<3.11.0

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-phangorn:

depends r-tidyr:

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-philr

and update with::

   mamba update bioconductor-philr

To create a new environment, run:

mamba create --name myenvname bioconductor-philr

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-philr:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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