recipe bioconductor-hmp2data

16s rRNA sequencing data from the Human Microbiome Project 2

Homepage:

https://bioconductor.org/packages/3.17/data/experiment/html/HMP2Data.html

License:

Artistic-2.0

Recipe:

/bioconductor-hmp2data/meta.yaml

HMP2Data is a Bioconductor package of the Human Microbiome Project 2 (HMP2) 16S rRNA sequencing data. Processed data is provided as phyloseq, SummarizedExperiment, and MultiAssayExperiment class objects. Individual matrices and data.frames used for building these S4 class objects are also provided in the package.

package bioconductor-hmp2data

versions:

1.14.0-0,  1.12.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.1.0-0,  1.0.0-0

depends bioconductor-annotationhub:

>=3.8.0,<3.9.0

depends bioconductor-data-packages:

>=20230706

depends bioconductor-experimenthub:

>=2.8.0,<2.9.0

depends bioconductor-multiassayexperiment:

>=1.26.0,<1.27.0

depends bioconductor-phyloseq:

>=1.44.0,<1.45.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends curl:

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-kableextra:

depends r-knitr:

depends r-magrittr:

depends r-readr:

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-hmp2data

and update with::

   mamba update bioconductor-hmp2data

To create a new environment, run:

mamba create --name myenvname bioconductor-hmp2data

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-hmp2data:<tag>

(see `bioconductor-hmp2data/tags`_ for valid values for ``<tag>``)

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Link to this page

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