recipe bioconductor-adapt

Analysis of Microbiome Differential Abundance by Pooling Tobit Models

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/ADAPT.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-adapt/meta.yaml

ADAPT carries out differential abundance analysis for microbiome metagenomics data in phyloseq format. It has two innovations. One is to treat zero counts as left censored and use Tobit models for log count ratios. The other is an innovative way to find non-differentially abundant taxa as reference, then use the reference taxa to find the differentially abundant ones.

package bioconductor-adapt

versions:

1.0.0-0

depends bioconductor-phyloseq:

>=1.50.0,<1.51.0

depends bioconductor-phyloseq:

>=1.50.0,<1.51.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-ggplot2:

>=3.4.1

depends r-ggrepel:

>=0.9.1

depends r-rcpp:

>=1.0.8

depends r-rcpparmadillo:

>=0.10.8

depends r-rcppparallel:

>=5.1.5

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-adapt

and update with::

   mamba update bioconductor-adapt

To create a new environment, run:

mamba create --name myenvname bioconductor-adapt

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-adapt:<tag>

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

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