# CoRegNet : reconstruction and integrated analysis of co-regulatory networks

## Documentation for package ‘CoRegNet’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.