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

bivar.awkSummary statistics from two variables
CeTF-classThe CeTF Class
CeTFdemoCeTFdemo class object example
CircosTargetsCircos plot for the Transcription Factors/genes targets.
clustCoefCalculate the clustering coefficient
clustCoefPercentageCalculate the clustering coefficient as a percentage
densityPlotDensity distribution of correlation coefficients and...
diffusionNetwork diffusion analysis
enrichdemoEnrichment data
enrichPlotPlots to visualize the enrichment analysis results
expDiffDifferential expression analysis
getData-methodsData accessor for a CeTF class object.
getDE-methodsDifferential Expression accessor for a CeTF class object.
getEnrichEnrichment analysis for genes of network
getGroupGOFunctional Profile of a gene set at specific GO level
heatPlotHeatmap-like functional classification
histPlotHistogram of connectivity distribution
InputData-methodsInput data accessor for a CeTF class object.
netConditionsPlotNetwork plot of gene-gene/gene-TFs interactions
netGOTFPlotPlot a network for Ontologies, genes and TFs
NetworkData-methodsNetworks data accessor for a CeTF class object.
normExpNormalized expression transformation
OutputData-methodsOutput data accessor for a CeTF class object.
PCITPartial Correlation and Information Theory (PCIT) analysis
pcitCA helper to calculate PCIT implemented in C/C++
refGenesList of reference genes for 5 different organisms to perform...
RIFRegulatory Impact Factors (RIF) analysis
RIF_inputRegulatory Impact Factors (RIF) input
RIFPlotRelationship plots between RIF1, RIF2 and DE genes
runAnalysisWhole analysis of Regulatory Impact Factors (RIF) and Partial...
simCountsSimulated counts data
simNormSimulated normalized data
SmearPlotSmear plot for Differentially Expressed genes and TFs
TFsTranscripition Factors data
toleranceTolerance level between 3 pairwise correlations implemented...
CeTF documentation built on Nov. 25, 2020, 2 a.m.