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netZooR

This is the development version of netZooR; for the stable release version, see netZooR.

Unified methods for the inference and analysis of gene regulatory networks


Bioconductor version: Development (3.19)

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.

Author: Marouen Ben Guebila [aut, cre] , Tian Wang [aut] , John Platig [aut], Marieke Kuijjer [aut] , Megha Padi [aut] , Rebekka Burkholz [aut], Des Weighill [aut] , Kate Shutta [aut]

Maintainer: Marouen Ben Guebila <marouen.b.guebila at gmail.com>

Citation (from within R, enter citation("netZooR")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("netZooR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("netZooR")
CONDOR HTML R Script
Reference Manual PDF

Details

biocViews GeneExpression, GeneRegulation, GraphAndNetwork, Microarray, Network, NetworkInference, Software, Transcription
Version 1.7.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.2.0), igraph, reticulate, pandaR, yarn, matrixcalc
Imports RCy3, viridisLite, STRINGdb, Biobase, GOstats, AnnotationDbi, matrixStats, GO.db, org.Hs.eg.db, Matrix, gplots, nnet, data.table, vegan, stats, utils, reshape, reshape2, penalized, parallel, doParallel, foreach, ggplot2, ggdendro, grid, MASS, assertthat, tidyr, methods, dplyr, graphics
System Requirements
URL https://github.com/netZoo/netZooR https://netzoo.github.io/
Bug Reports https://github.com/netZoo/netZooR/issues
See More
Suggests testthat (>= 2.1.0), knitr, rmarkdown, pkgdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package netZooR_1.7.0.tar.gz
Windows Binary netZooR_1.7.0.zip
macOS Binary (x86_64) netZooR_1.7.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/netZooR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/netZooR
Bioc Package Browser https://code.bioconductor.org/browse/netZooR/
Package Short Url https://bioconductor.org/packages/netZooR/
Package Downloads Report Download Stats