netZooR
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This is the released version of netZooR; for the devel version, see netZooR.
A menagerie of methods for the inference and analysis of gene regulatory networks
Bioconductor version: Release (3.23)
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: Tara Eicher [aut] 
, Marouen Ben Guebila [aut, cre] , Tian Wang [aut] , John Platig [aut], Marieke Kuijjer [aut] , Megha Padi [aut] , Rebekka Burkholz [aut], Des Weighill [aut] , Chen Chen [aut] , Kate Shutta [aut]
Maintainer: Marouen Ben Guebila <marouen.b.guebila at gmail.com>
citation("netZooR")):Tara Eicher, Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Des Weighill, Chen Chen, Kate Shutta. netZooR: A menagerie of methods for the inference and analysis of gene regulatory networks. doi:10.18129/B9.bioc.netZooR, R package version 1.16.0, https://bioconductor.org/packages/netZooR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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")| Using CONDOR for community detection in bipartite graphs | HTML |
| Reference Manual |
Details
| biocViews | GeneExpression, GeneRegulation, GraphAndNetwork, Microarray, Network, NetworkInference, Software, Transcription |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.2.0), igraph, reticulate, pandaR, Biobase |
| Imports | cmdstanr, AnnotationDbi, assertthat, biomaRt, cmdstanr, corpcor, data.table, doParallel, downloader, dplyr, edgeR, foreach, GeneNet, ggdendro, ggplot2, GO.db, GOstats, gplots, graphics, grid, limma, loo, MASS, Matrix, matrixcalc, matrixStats, matrixTests, methods, nnet, org.Hs.eg.db, parallel, penalized, preprocessCore, quantro, rARPACK, RColorBrewer, RCy3, readr, reshape, reshape2, stats, STRINGdb, tidyr, utils, vegan, viridisLite |
| System Requirements | |
| URL | https://github.com/netZoo/netZooR https://netzoo.github.io/ |
| Bug Reports | https://github.com/netZoo/netZooR/issues |
See More
| Suggests | dorothea, knitr, pkgdown, rmarkdown, testthat (>= 2.1.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-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 |