GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data

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Documentation for package ‘GeneNetworkBuilder’ version 1.48.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

GeneNetworkBuilder-package	Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
browseNetwork	browse network
browseNetwork-shiny	Shiny bindings for browseNetwork
browseNetworkOutput	Shiny bindings for browseNetwork
buildNetwork	construct the regulatory network
ce.IDsMap	C.elegns gene name to wormbase identifier map
ce.interactionmap	transcript regulatory map of _Caenorhabditis elegans_
ce.mapIDs	map file for converting from wormbase identifier to _Caenorhabditis elegans_ gene name
ce.miRNA.map	micro RNA of _Caenorhabditis elegans_
convertID	convert gene IDs by id map
cy3Network	visualize the network by Cy3
example.data	example datasets for documentation
exportNetwork	Save network in various formats
filterNetwork	filter the regulatory network table by expression profile
GeneNetworkBuilder	Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
hs.IDsMap	map file for converting gene name or sequence name of _Homo sapiens_ to Entrez identifier
hs.interactionmap	transcript regulation map of _Homo sapiens_
hs.mapIDs	map file for converting from Entrez identifier to _Homo sapiens_ gene name
hs.miRNA.map	micro RNA of _Homo sapiens_
networkFromGenes	Build network by a list of given genes
polishNetwork	generate an object of grahpNEL to represent the regulation network
renderBrowseNetwork	Shiny bindings for browseNetwork
saveXGMML	Save network as xgmml
subsetNetwork	Subset a polished network
uniqueExprsData	unique the microarray data