bivar.awk |
Summary statistics from two variables |
CeTF |
The CeTF Class |
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 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. |
getData-method |
Data accessor for a CeTF class object. |
getDE |
Differential Expression accessor for a CeTF class object. |
getDE-method |
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 |
Input data accessor for a CeTF class object. |
InputData-method |
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. |
NetworkData-method |
Networks data accessor for a CeTF class object. |
normExp |
Normalized expression transformation |
OutputData |
Output data accessor for a CeTF class object. |
OutputData-method |
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 |
Regulatory Impact Factors (RIF) analysis |
RIFPlot |
Relationship plots between RIF1, RIF2 and DE genes |
RIF_input |
Regulatory Impact Factors (RIF) input |
runAnalysis |
Whole analysis of Regulatory Impact Factors (RIF) and Partial Correlation and Information Theory analysis (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++ |