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