- 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:
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
r-base
>=4.2,<4.3.0a0
- 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¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-curatedmetagenomicdata/README.html)