recipe bioconductor-curatedmetagenomicdata

Curated Metagenomic Data of the Human Microbiome

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/curatedMetagenomicData.html

License:

Artistic-2.0

Recipe:

/bioconductor-curatedmetagenomicdata/meta.yaml

The curatedMetagenomicData package provides standardized, curated human microbiome data for novel analyses. It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. The bacterial, fungal, and archaeal taxonomic abundances for each sample were calculated with MetaPhlAn3, and metabolic functional potential was calculated with HUMAnN3. The manually curated sample metadata and standardized metagenomic data are available as (Tree)SummarizedExperiment objects.

package bioconductor-curatedmetagenomicdata

versions:

3.10.0-0,  3.8.0-0,  3.6.0-0,  3.4.1-0,  3.2.3-0,  3.2.1-0,  3.0.1-0,  1.20.0-1,  1.20.0-0, 

3.10.0-0,  3.8.0-0,  3.6.0-0,  3.4.1-0,  3.2.3-0,  3.2.1-0,  3.0.1-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.1-0,  1.12.3-0,  1.10.2-0,  1.8.1-0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-experimenthub:

>=2.10.0,<2.11.0

depends bioconductor-mia:

>=1.10.0,<1.11.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-treesummarizedexperiment:

>=2.10.0,<2.11.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-magrittr:

depends r-purrr:

depends r-rlang:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

depends r-tidyselect:

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-curatedmetagenomicdata

and update with::

   mamba update bioconductor-curatedmetagenomicdata

To create a new environment, run:

mamba create --name myenvname bioconductor-curatedmetagenomicdata

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-curatedmetagenomicdata:<tag>

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

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