DOI: 10.18129/B9.bioc.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(,the R implementation of CONDOR( and the R implementation of 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>

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biocViews GeneExpression, GeneRegulation, GraphAndNetwork, Microarray, Network, NetworkInference, Software, Transcription
Version 1.0.0
In Bioconductor since BioC 3.15 (R-4.2) (0.5 years)
License GPL-3
Depends R (>= 4.1.0), igraph, reticulate, pandaR, yarn
Imports RCy3, viridisLite, STRINGdb, Biobase, GOstats, AnnotationDbi, matrixStats, GO.db,, Matrix, gplots, nnet, data.table, vegan, stats, utils, reshape, reshape2, penalized, parallel, doParallel, foreach, ggplot2, ggdendro, grid, MASS, assertthat, tidyr, methods, dplyr, graphics
Suggests testthat (>= 2.1.0), knitr, rmarkdown, pkgdown
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