Table 1 Functions available in CeTF
Function | Description |
|---|---|
bivar.awk | Summary statistics from two variables |
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 significant PCIT values |
diffusion | Network diffusion analysis |
enrichdemo | Enrichment data |
enrichPlot | Plots to visualize the enrichment analysis results |
expDiff | Differential expression analysis |
getData | Data accessor for a CeTF class object |
getDE | 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 |
heatPlot | Heatmap-like functional classification |
histPlot | Histogram of connectivity distribution |
InputData | 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 | Networks data accessor for a CeTF class object |
normExp | Normalized expression transformation |
OutputData | 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 enrichment |
RIF_input | Regulatory Impact Factors (RIF) input |
RIF | Regulatory Impact Factors (RIF) analysis |
RIFPlot | Relationship plots between RIF1, RIF2 and DE genes |
runAnalysis | Whole analysis of RIF and PCIT |
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 in C/C++ |