Package Recipe 'bioconductor-netzoor'

recipe bioconductor-netzoor

Unified methods for the inference and analysis of gene regulatory networks

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/netZooR.html
License:: GPL-3
Recipe:: /bioconductor-netzoor/meta.yaml

netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.

package bioconductor-netzoor¶

Versions:

1.14.1-0, 1.10.0-0, 1.6.0-0, 1.4.0-0, 1.2.0-0

Depends:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-pandar >=1.42.0,<1.43.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-doparallel
on r-foreach
on r-igraph
on r-mass
on r-matrix
on r-matrixstats
on r-reshape
on r-reticulate

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-netzoor

to add into an existing workspace instead, run:

pixi add bioconductor-netzoor

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-netzoor

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-netzoor

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-netzoor:<tag>

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