CeTF-class              The CeTF Class
CeTFdemo                CeTFdemo class object example
CircosTargets           Circos plot for the Transcription Factors/genes
                        targets.
InputData               Input data accessor for a CeTF class object.
NetworkData             Networks data accessor for a CeTF class object.
OutputData              Output data accessor for a CeTF class object.
PCIT                    Partial Correlation and Information Theory
                        (PCIT) analysis
RIF                     Regulatory Impact Factors (RIF) analysis
RIFPlot                 Relationship plots between RIF1, RIF2 and DE
                        genes
RIF_input               Regulatory Impact Factors (RIF) input
SmearPlot               Smear plot for Differentially Expressed genes
                        and TFs
TFs                     Transcripition Factors data
bivar.awk               Summary statistics from two variables
clustCoef               Calculate the clustering coefficient
clustCoefPercentage     Calculate the clustering coefficient as a
                        percentage
densityPlot             Density distribution of correlation
                        coefficients and significant PCIT values
diffusion               Network diffusion analysis
enrichPlot              Plots to visualize the enrichment analysis
                        results
enrichdemo              Enrichment data
expDiff                 Differential expression analysis
getDE                   Differential Expression accessor for a CeTF
                        class object.
getData                 Data 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
netConditionsPlot       Network plot of gene-gene/gene-TFs interactions
netGOTFPlot             Plot a network for Ontologies, genes and TFs
normExp                 Normalized expression transformation
pcitC                   A helper to calculate PCIT implemented in C/C++
refGenes                List of reference genes for 5 different
                        organisms to perform enrichment
runAnalysis             Whole analysis of Regulatory Impact Factors
                        (RIF) and Partial Correlation and Information
                        Theory analysis (PCIT)
simCounts               Simulated counts data
simNorm                 Simulated normalized data
tolerance               Tolerance level between 3 pairwise correlations
                        implemented in C/C++
