netZooR

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see netZooR.

Unified methods for the inference and analysis of gene regulatory networks

Bioconductor version: 3.20

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 iD ORCID: 0000-0001-5934-966X , Tian Wang [aut] ORCID iD ORCID: 0000-0002-2767-3243 , John Platig [aut], Marieke Kuijjer [aut] ORCID iD ORCID: 0000-0001-6280-3130 , Megha Padi [aut] ORCID iD ORCID: 0000-0002-3446-4562 , Rebekka Burkholz [aut], Des Weighill [aut] ORCID iD ORCID: 0000-0003-4979-5871 , Kate Shutta [aut] ORCID iD ORCID: 0000-0003-0402-3771

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")
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

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, GeneRegulation, GraphAndNetwork, Microarray, Network, NetworkInference, Software, Transcription

Version 1.10.0

In Bioconductor since BioC 3.15 (R-4.2) (3 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

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Package Archives

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

Source Package netZooR_1.10.0.tar.gz

Windows Binary (x86_64) netZooR_1.10.0.zip (64-bit only)

macOS Binary (x86_64) netZooR_1.10.0.tgz

macOS Binary (arm64) netZooR_1.10.0.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/

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