Package Recipe 'bioconductor-curatedmetagenomicdata'

recipe bioconductor-curatedmetagenomicdata

Curated Metagenomic Data of the Human Microbiome

Homepage:: https://bioconductor.org/packages/3.20/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:

3.18.0-0, 3.14.0-0, 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,

3.18.0-0, 3.14.0-0, 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:

on bioconductor-annotationhub >=4.0.0,<4.1.0
on bioconductor-data-packages >=20260207
on bioconductor-experimenthub >=3.0.0,<3.1.0
on bioconductor-mia >=1.18.0,<1.19.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-treesummarizedexperiment >=2.18.0,<2.19.0
on curl
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-magrittr
on r-purrr
on r-rlang
on r-stringr
on r-tibble
on r-tidyr
on r-tidyselect

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-curatedmetagenomicdata

to add into an existing workspace instead, run:

pixi add bioconductor-curatedmetagenomicdata

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-curatedmetagenomicdata

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-curatedmetagenomicdata

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

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