netZooR

DOI: 10.18129/B9.bioc.netZooR  

Unified methods for the inference and analysis of gene regulatory networks

Bioconductor version: Release (3.16)

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 [ctb]

Maintainer: Marouen Ben Guebila <benguebila at hsph.harvard.edu>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	CONDOR
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GeneRegulation, GraphAndNetwork, Microarray, Network, NetworkInference, Software, Transcription
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	GPL-3
Depends	R (>= 4.2.0), igraph, reticulate, pandaR, yarn
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
LinkingTo
Suggests	testthat (>= 2.1.0), knitr, rmarkdown, pkgdown
SystemRequirements
Enhances
URL	https://github.com/netZoo/netZooR https://netzoo.github.io/
BugReports	https://github.com/netZoo/netZooR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	netZooR_1.2.0.tar.gz
Windows Binary	netZooR_1.2.0.zip
macOS Binary (x86_64)	netZooR_1.2.0.tgz
macOS Binary (arm64)	netZooR_1.2.0.tgz
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