netZooR

A menagerie of methods for the inference and analysis of gene regulatory networks

Bioconductor version: 3.23 · Package version: 1.16.0

Other Bioconductor versions

devel is the development version; release is the current stable one.

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.

DOI: 10.18129/B9.bioc.netZooR

Installation

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

BiocManager::install("netZooR")

Details

Maintainer	Marouen Ben Guebila <marouen.b.guebila@gmail.com>
Author	Tara Eicher [aut] (ORCID: <https://orcid.org/0000-0003-1809-4458>), Marouen Ben Guebila [aut, cre] (ORCID: <https://orcid.org/0000-0001-5934-966X>), Tian Wang [aut] (ORCID: <https://orcid.org/0000-0002-2767-3243>), John Platig [aut], Marieke Kuijjer [aut] (ORCID: <https://orcid.org/0000-0001-6280-3130>), Megha Padi [aut] (ORCID: <https://orcid.org/0000-0002-3446-4562>), Rebekka Burkholz [aut], Des Weighill [aut] (ORCID: <https://orcid.org/0000-0003-4979-5871>), Chen Chen [aut] (ORCID: <https://orcid.org/0000-0002-8042-7201>), Kate Shutta [aut] (ORCID: <https://orcid.org/0000-0003-0402-3771>)
License	GPL-3
URL	https://github.com/netZoo/netZooR, https://netzoo.github.io/
Bug Reports	https://github.com/netZoo/netZooR/issues
Status	Deprecated
Source branch	RELEASE_3_23
Build report	Bioconductor build system, r-universe
biocViews	GeneExpression, GeneRegulation, GraphAndNetwork, Microarray, Network, NetworkInference, Software, Transcription
Package Short Url	https://bioconductor.org/packages/netZooR/

Citation

From within R, enter 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.

Documentation

Using CONDOR for community detection in bipartite graphs

Dependencies

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

Suggests: dorothea, knitr, pkgdown, rmarkdown, testthat (>= 2.1.0)