twangxxx/netZoo: Integrate methods: PANDA, LIONESS, CONDOR, ALPACA into one workflow.

PANDA(Passing Attributes between Networks for Data Assimilation) is a message-passing model to gene regulatory network reconstruction. It integrates multiple sources of biological data, including protein-protein interaction, gene expression, and sequence motif information, in order 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.

install.packages("remotes")
remotes::install_github("twangxxx/netZoo")