Package Recipe 'bioconductor-ppinfer'

recipe bioconductor-ppinfer

Inferring functionally related proteins using protein interaction networks

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/PPInfer.html
License:: Artistic-2.0
Recipe:: /bioconductor-ppinfer/meta.yaml

Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at identifying proteins closely related to some interesting proteins. A network based statistical learning method is used to infer the putative functions of proteins from the known functions of its neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions.

package bioconductor-ppinfer¶

Versions:

1.36.0-0, 1.32.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-1, 1.16.0-0,

1.36.0-0, 1.32.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-1, 1.16.0-0, 1.14.0-0, 1.12.0-1, 1.10.0-1, 1.8.1-1, 1.8.1-0, 1.6.0-0, 1.4.0-0, 1.2.4-0

Depends:

on bioconductor-biomart >=2.66.0,<2.67.0
on bioconductor-fgsea >=1.36.0,<1.37.0
on bioconductor-stringdb >=2.22.0,<2.23.0
on bioconductor-yeastexpdata >=0.56.0,<0.57.0
on r-base >=4.5,<4.6.0a0
on r-ggplot2
on r-httr
on r-igraph
on r-kernlab

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-ppinfer

to add into an existing workspace instead, run:

pixi add bioconductor-ppinfer

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-ppinfer

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-ppinfer

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-ppinfer:<tag>

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