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netZooR
This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see netZooR.
Integrate methods: PANDA, LIONESS, CONDOR, ALPACA, SAMBAR, MONSTER, OTTER, EGRET, and YARN into one workflow
Bioconductor version: 3.15
PANDA(Passing Attributes between Networks for Data Assimilation) is a message-passing model to reconstruction gene regulatory network. It integrates multiple sources of biological data, including protein-protein interaction data, gene expression data, and sequence motif information to reconstruct genome-wide, condition-specific regulatory networks.[(Glass et al. 2013)]. LIONESS(Linear Interpolation to Obtain Network Estimates for Single Samples) is a method to estimate sample-specific regulatory networks by applying linear interpolation to the predictions made by existing aggregate network inference approaches. CONDOR(COmplex Network Description Of Regulators)is a bipartite community structure analysis tool of biological networks, especially eQTL networks, including a method for scoring nodes based on their modularity contribution.[(Platig et al. 2016). ALPACA(ALtered Partitions Across Community Architectures) is a method for comparing two genome-scale networks derived from different phenotypic states to identify condition-specific modules.[(Padi and Quackenbush 2018)]. This package integrates pypanda--the Python implementation of PANDA and LIONESS(https://github.com/davidvi/pypanda),the R implementation of CONDOR(https://github.com/jplatig/condor) and the R implementation of ALPACA (https://github.com/meghapadi/ALPACA) into one workflow. Each tool can be call in this package by one function, and the relevant output could be accessible in current R session for downstream analysis.
Author: Tian Wang [aut], Marouen Ben Guebila [aut, cre], John Platig [aut], Marieke Kuijjer [aut], Magha Padi [aut], Rebekka Burkholz [aut], Deborah Weighill [aut]
Maintainer: Marouen Ben Guebila <marouen.b.guebila at gmail.com>
citation("netZooR")):
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")
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Follow Installation instructions to use this package in your R session.