recipe bioconductor-hmp16sdata

16S rRNA Sequencing Data from the Human Microbiome Project

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/HMP16SData.html

License:

Artistic-2.0

Recipe:

/bioconductor-hmp16sdata/meta.yaml

HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub.

package bioconductor-hmp16sdata

versions:

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0, 

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.1-0,  1.2.0-0

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-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends curl:

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-kableextra:

depends r-knitr:

depends r-magrittr:

depends r-readr:

depends r-stringr:

depends r-tibble:

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-hmp16sdata

and update with::

   mamba update bioconductor-hmp16sdata

To create a new environment, run:

mamba create --name myenvname bioconductor-hmp16sdata

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-hmp16sdata:<tag>

(see `bioconductor-hmp16sdata/tags`_ for valid values for ``<tag>``)

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