| 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... |
