Package Recipe 'bioconductor-bugphyzz'

recipe bioconductor-bugphyzz

A harmonized data resource and software for enrichment analysis of microbial physiologies

Homepage:: https://bioconductor.org/packages/3.20/data/experiment/html/bugphyzz.html
License:: Artistic-2.0
Recipe:: /bioconductor-bugphyzz/meta.yaml

bugphyzz is an electronic database of standardized microbial annotations. It facilitates the creation of microbial signatures based on shared attributes, which are utilized for bug set enrichment analysis. The data also includes annotations imputed with ancestra state reconstruction methods.

package bioconductor-bugphyzz¶

Versions:

1.4.0-0, 1.0.0-0

Depends:

on bioconductor-biocfilecache >=3.0.0,<3.1.0
on bioconductor-data-packages >=20260207
on bioconductor-s4vectors >=0.48.0,<0.49.0
on curl
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-httr2
on r-purrr
on r-stringr
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-bugphyzz

to add into an existing workspace instead, run:

pixi add bioconductor-bugphyzz

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-bugphyzz

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-bugphyzz

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-bugphyzz:<tag>

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