recipe bioconductor-netzoor

Unified methods for the inference and analysis of gene regulatory networks

Homepage:

https://bioconductor.org/packages/3.16/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:

1.2.0-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-go.db >=3.16.0,<3.17.0

• bioconductor-gostats >=2.64.0,<2.65.0

• bioconductor-org.hs.eg.db >=3.16.0,<3.17.0

• bioconductor-pandar >=1.30.0,<1.31.0

• bioconductor-rcy3 >=2.18.0,<2.19.0

• bioconductor-stringdb >=2.10.0,<2.11.0

• bioconductor-yarn >=1.24.0,<1.25.0

• r-assertthat

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-doparallel

• r-dplyr

• r-foreach

• r-ggdendro

• r-ggplot2

• r-gplots

• r-igraph

• r-mass

• r-matrix

• r-matrixstats

• r-nnet

• r-penalized

• r-reshape

• r-reshape2

• r-reticulate

• r-tidyr

• r-vegan

• r-viridislite

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-netzoor

and update with:

conda update bioconductor-netzoor

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-netzoor:<tag>

(see bioconductor-netzoor/tags for valid values for <tag>)

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)