Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

bivar.awk | Summary statistics from two variables |

CeTF-class | The CeTF Class |

CeTFdemo | CeTFdemo class object example |

CircosTargets | Circos plot for the Transcription Factors/genes targets. |

clustCoef | Calculate the clustering coefficient |

clustCoefPercentage | Calculate the clustering coefficient as a percentage |

densityPlot | Density distribution of correlation coefficients and... |

diffusion | Network diffusion analysis |

enrichdemo | Enrichment data |

enrichPlot | Plots to visualize the enrichment analysis results |

expDiff | Differential expression analysis |

getData-methods | Data accessor for a CeTF class object. |

getDE-methods | Differential Expression accessor for a CeTF class object. |

getEnrich | Enrichment analysis for genes of network |

getGroupGO | Functional Profile of a gene set at specific GO level |

gtfToBed | Converts GTF to BED |

heatPlot | Heatmap-like functional classification |

histPlot | Histogram of connectivity distribution |

InputData-methods | Input data accessor for a CeTF class object. |

netConditionsPlot | Network plot of gene-gene/gene-TFs interactions |

netGOTFPlot | Plot a network for Ontologies, genes and TFs |

NetworkData-methods | Networks data accessor for a CeTF class object. |

normExp | Normalized expression transformation |

OutputData-methods | Output data accessor for a CeTF class object. |

PCIT | Partial Correlation and Information Theory (PCIT) analysis |

pcitC | A helper to calculate PCIT implemented in C/C++ |

refGenes | List of reference genes for 5 different organisms to perform... |

RIF | Regulatory Impact Factors (RIF) analysis |

RIF_input | Regulatory Impact Factors (RIF) input |

RIFPlot | Relationship plots between RIF1, RIF2 and DE genes |

runAnalysis | Whole analysis of Regulatory Impact Factors (RIF) and Partial... |

simCounts | Simulated counts data |

simNorm | Simulated normalized data |

SmearPlot | Smear plot for Differentially Expressed genes and TFs |

TFs | Transcripition Factors data |

tolerance | Tolerance level between 3 pairwise correlations implemented... |

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