Package Recipe 'bioconductor-anansi'

recipe bioconductor-anansi

Annotation-Based Analysis of Specific Interactions

Homepage:: https://bioconductor.org/packages/3.22/bioc/html/anansi.html
License:: GPL-3
Recipe:: /bioconductor-anansi/meta.yaml

Studies including both microbiome and metabolomics data are becoming more common. Often, it would be helpful to integrate both datasets in order to see if they corroborate each others patterns. All vs all association is imprecise and likely to yield spurious associations. This package takes a knowledge-based approach to constrain association search space, only considering metabolite-function pairs that have been recorded in a pathway database. This package also provides a framework to assess differential association.

package bioconductor-anansi¶

Versions:

1.0.0-0

Depends:

on bioconductor-multiassayexperiment >=1.36.0,<1.37.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-treesummarizedexperiment >=2.18.0,<2.19.0
on r-base >=4.5,<4.6.0a0
on r-forcats
on r-ggforce
on r-ggplot2
on r-ggraph
on r-igraph
on r-matrix
on r-patchwork
on r-rlang
on r-s7
on r-tidygraph

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-anansi

to add into an existing workspace instead, run:

pixi add bioconductor-anansi

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-anansi

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-anansi

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-anansi:<tag>

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