recipe bioconductor-path2ppi

Prediction of pathway-related protein-protein interaction networks

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/Path2PPI.html

License:

GPL (>= 2)

Recipe:

/bioconductor-path2ppi/meta.yaml

Links:

biotools: path2ppi

Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins.

package bioconductor-path2ppi

(downloads) docker_bioconductor-path2ppi

Versions:
1.40.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0, 

1.40.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-0

Depends:

  • on r-base >=4.5,<4.6.0a0

  • on r-igraph >=1.0.1

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-path2ppi

to add into an existing workspace instead, run:

pixi add bioconductor-path2ppi

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-path2ppi

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-path2ppi

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-path2ppi:<tag>

(see bioconductor-path2ppi/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.

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