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| assoScore | Association scores for gene pairs |
| Bakal2007 | Rich morphological phenotypes for gene overexpression and RNA interference screens |
| Bakal2007Cluster | Rich morphological phenotypes for gene overexpression and RNA interference screens |
| BetaMixture | An S4 class for beta mixture modelling of functional gene associations |
| BetaMixture-class | An S4 class for beta mixture modelling of functional gene associations |
| bm1 | Rich morphological phenotypes for gene overexpression and RNA interference screens |
| buildPAN | Build an igraph or RedeR graph for PAN |
| buildPAN-method | Build an igraph or RedeR graph for PAN |
| cosineDist | Compute cosine similarities or distances between pairs of genes |
| cosineSim | Compute cosine similarities or distances between pairs of genes |
| exportPAN | Export inferred PAN or module graphs to files |
| exportPAN-method | Export inferred PAN or module graphs to files |
| fitBM | Fit a three-beta mixture model to densities of functional gene associations |
| fitBM-method | Fit a three-beta mixture model to densities of functional gene associations |
| fitNULL | Fit the NULL component of a three-beta mixture model for functional gene associations |
| fitNULL-method | Fit the NULL component of a three-beta mixture model for functional gene associations |
| infer | Infer a posterior association network |
| infer-method | Infer a posterior association network |
| nodeColor | Rich morphological phenotypes for gene overexpression and RNA interference screens |
| p2SNR | Translate p-values to Signal-to-Noise Ratios |
| p2SNR-method | Translate p-values to Signal-to-Noise Ratios |
| PAN | An S4 class for inferring a posterior association network |
| PAN-class | An S4 class for inferring a posterior association network |
| pvclustModule | Search enriched functional gene modules by pvclust |
| pvclustModule-method | Search enriched functional gene modules by pvclust |
| sigModules | Retrieve ids for significant gene modules searched by pvclust |
| sigModules-method | Retrieve ids for significant gene modules searched by pvclust |
| SNR2p | Translate p-values to Signal-to-Noise Ratios |
| SNR2p-method | Translate p-values to Signal-to-Noise Ratios |
| summarize | Summarize the object of S4 class 'BetaMixture' or 'PAN' |
| summarize-method | Summarize the object of S4 class 'BetaMixture' or 'PAN' |
| view | View the results of beta-mixture model fitting |
| view-method | View the results of beta-mixture model fitting |
| viewLegend | View the legends for the graph built for PAN |
| viewLegend-method | View the legends for the graph built for PAN |
| viewNestedModules | View the nested modules in a posterior association network in RedeR |
| viewNestedModules-method | View the nested modules in a posterior association network in RedeR |
| viewPAN | Show posterior association networks or modules in 'igraph' or 'RedeR' |
| viewPAN-method | Show posterior association networks or modules in 'igraph' or 'RedeR' |