CoRegNet : reconstruction and integrated analysis of co-regulatory networks

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Documentation for package ‘CoRegNet’ version 1.28.0

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coRegnet-package coRegnet : inference and interrogation co-regulation networks
activators Interogate a coregnet object.
activators-method Interogate a coregnet object.
addCooperativeEvidences Integration of regulatory evidences.
addCooperativeEvidences-method Integration of regulatory evidences.
addEvidences Integration of regulatory evidences.
addEvidences-method Integration of regulatory evidences.
CHEA_sub Human Transcription Factor data and Bladder cancer dataset.
CIT_BLCA_CNV Human Transcription Factor data and Bladder cancer dataset.
CIT_BLCA_EXP Human Transcription Factor data and Bladder cancer dataset.
CIT_BLCA_Subgroup Human Transcription Factor data and Bladder cancer dataset.
coRegnet coRegnet : inference and interrogation co-regulation networks
coregnet Initialize a co-regulatory network object.
coregnet-class Class coregnet - Specifying the structure of the network used throughout the package.
coregnetToDataframe Summaries and info coregnet
coregnetToDataframe-method Summaries and info coregnet
coregnetToList Summaries and info coregnet
coregnetToList-method Summaries and info coregnet
coregnetToList.CoRegNet Summaries and info coregnet
coregnetToList.coregnet Summaries and info coregnet
coregulators Extract all co-regulators of a regulatory network.
coregulators-method Extract all co-regulators of a regulatory network.
dim-method Summaries and info coregnet
discretizeExpressionData Three-value discretization of gene expression data.
display Display a shiny interactive web interface to
ENCODE_sub Human Transcription Factor data and Bladder cancer dataset.
HIPPIE_sub Human Transcription Factor data and Bladder cancer dataset.
hLICORN Hybrid Learning of co-operative regulation network.
HumanTF List of Human Transcription Factors.
HumanTF_entrezgene List of Human Transcription Factors.
length-method Summaries and info coregnet
masterRegulator Identify phenotype related Master Regulators.
masterRegulator-method Identify phenotype related Master Regulators.
print-method Summaries and info coregnet
refine Refine an inferred regulatory network using external evidence.
refine-method Refine an inferred regulatory network using external evidence.
regulatorInfluence Regulator Influence, estimating the sample specific activity of Transcription Factors.
regulatorInfluence-method Regulator Influence, estimating the sample specific activity of Transcription Factors.
regulators Interogate a coregnet object.
regulators-method Interogate a coregnet object.
repressors Interogate a coregnet object.
repressors-method Interogate a coregnet object.
show-method Summaries and info coregnet
STRING_sub Human Transcription Factor data and Bladder cancer dataset.
summary Summaries and info coregnet
summary-method Summaries and info coregnet
targets Interogate a coregnet object.
targets-method Interogate a coregnet object.