Package Recipe 'bioconductor-hmp2data'

recipe bioconductor-hmp2data

16s rRNA sequencing data from the Human Microbiome Project 2

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

1.20.0-0, 1.16.0-0, 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,

1.20.0-0, 1.16.0-0, 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:

on bioconductor-annotationhub >=3.14.0,<3.15.0
on bioconductor-data-packages >=20241103
on bioconductor-experimenthub >=2.14.0,<2.15.0
on bioconductor-multiassayexperiment >=1.32.0,<1.33.0
on bioconductor-phyloseq >=1.50.0,<1.51.0
on bioconductor-s4vectors >=0.44.0,<0.45.0
on bioconductor-summarizedexperiment >=1.36.0,<1.37.0
on curl
on r-assertthat
on r-base >=4.4,<4.5.0a0
on r-data.table
on r-dplyr
on r-kableextra
on r-knitr
on r-magrittr
on r-readr

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-hmp2data

to add into an existing workspace instead, run:

pixi add bioconductor-hmp2data

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-hmp2data

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-hmp2data

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-hmp2data:<tag>

(see bioconductor-hmp2data/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-hmp2data/README.html)