Package Recipe 'bioconductor-pi'

recipe bioconductor-pi

Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

Homepage:: https://bioconductor.org/packages/3.18/bioc/html/Pi.html
License:: GPL-3
Recipe:: /bioconductor-pi/meta.yaml

Priority index or Pi is developed as a genomic-led target prioritisation system. It integrates functional genomic predictors, knowledge of network connectivity and immune ontologies to prioritise potential drug targets at the gene and pathway level.

package bioconductor-pi¶

Versions:

2.14.0-0, 2.12.0-0, 2.10.0-0, 2.6.0-0, 2.4.0-0, 2.2.0-0, 2.0.0-0, 1.14.0-0, 1.12.0-1,

2.14.0-0, 2.12.0-0, 2.10.0-0, 2.6.0-0, 2.4.0-0, 2.2.0-0, 2.0.0-0, 1.14.0-0, 1.12.0-1, 1.10.0-0

Depends:

on bioconductor-biocgenerics >=0.48.0,<0.49.0
on bioconductor-genomeinfodb >=1.38.0,<1.39.0
on bioconductor-genomicranges >=1.54.0,<1.55.0
on bioconductor-iranges >=2.36.0,<2.37.0
on bioconductor-suprahex >=1.40.0,<1.41.0
on r-base >=4.3,<4.4.0a0
on r-caret
on r-dnet
on r-dplyr
on r-ggnetwork
on r-ggplot2
on r-ggrepel
on r-glmnet
on r-igraph
on r-lattice
on r-mass
on r-matrix
on r-osfr
on r-plot3d
on r-purrr
on r-randomforest
on r-rcircos
on r-readr
on r-rocr
on r-scales
on r-tibble
on r-tidyr

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-pi

to add into an existing workspace instead, run:

pixi add bioconductor-pi

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-pi

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-pi

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-pi:<tag>

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