recipe bioconductor-pathifier

Quantify deregulation of pathways in cancer

Homepage:

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

License:

Artistic-1.0

Recipe:

/bioconductor-pathifier/meta.yaml

Links:

biotools: pathifier, doi: 10.1073/pnas.1219651110

Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.

package bioconductor-pathifier

(downloads) docker_bioconductor-pathifier

Versions:
1.48.0-0,  1.44.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0, 

1.48.0-0,  1.44.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.16.0-0

Depends:

  • on r-base >=4.5,<4.6.0a0

  • on r-princurve >=2.0.4

  • on r-r.oo

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-pathifier

to add into an existing workspace instead, run:

pixi add bioconductor-pathifier

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-pathifier

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-pathifier

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-pathifier:<tag>

(see bioconductor-pathifier/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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