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 (3.21)

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] (ORCID: ), Tian Wang [aut] (ORCID: ), John Platig [aut], Marieke Kuijjer [aut] (ORCID: ), Megha Padi [aut] (ORCID: ), Rebekka Burkholz [aut], Des Weighill [aut] (ORCID: ), Kate Shutta [aut] (ORCID: )

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 "4.5") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, GeneRegulation, GraphAndNetwork, Microarray, Network, NetworkInference, Software, Transcription
Version	1.11.0
In Bioconductor since	BioC 3.15 (R-4.2) (2.5 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

Suggests	testthat (>= 2.1.0), knitr, rmarkdown, pkgdown
Linking To
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Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/netZooR/
Package Downloads Report	Download Stats