Package Recipe 'bioconductor-bionar'

recipe bioconductor-bionar

Biological Network Analysis in R

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

the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of diseases across the network and specific clusters pointing towards shared/common mechanisms.

package bioconductor-bionar¶

Versions:

1.12.2-0, 1.8.0-0, 1.4.0-0, 1.2.4-0, 1.0.0-0

Depends:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-fgsea >=1.36.0,<1.37.0
on bioconductor-go.db >=3.22.0,<3.23.0
on bioconductor-org.hs.eg.db >=3.22.0,<3.23.0
on r-base >=4.5,<4.6.0a0
on r-cowplot
on r-data.table
on r-dplyr
on r-ggplot2
on r-ggrepel
on r-igraph >=2.0.1.1
on r-latex2exp
on r-matrix
on r-minpack.lm
on r-powerlaw
on r-rdpack
on r-rspectra
on r-rspectral
on r-scales
on r-stringr
on r-viridis
on r-wgcna

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-bionar

to add into an existing workspace instead, run:

pixi add bioconductor-bionar

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-bionar

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-bionar

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-bionar:<tag>

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