recipe bioconductor-curatedmetagenomicdata

Curated Metagenomic Data of the Human Microbiome

Homepage:

https://bioconductor.org/packages/3.16/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:

3.6.0-0,  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, 

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 >=3.6.0,<3.7.0

• bioconductor-data-packages >=20221108

• bioconductor-experimenthub >=2.6.0,<2.7.0

• bioconductor-mia >=1.6.0,<1.7.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• bioconductor-treesummarizedexperiment >=2.6.0,<2.7.0

• curl

• r-base >=4.2,<4.3.0a0

• r-dplyr

• r-magrittr

• r-purrr

• r-rlang

• r-stringr

• r-tibble

• r-tidyr

• r-tidyselect

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-curatedmetagenomicdata

and update with:

conda update bioconductor-curatedmetagenomicdata

or use the docker container:

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

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

Download stats

Link to this page

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-curatedmetagenomicdata/README.html)