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| association | Association |
| clusterEnrichment | Term enrichment |
| clusterEnrichment-method | Term enrichment |
| clusterVisualization | Displays graphs of the differentially expressed clusters |
| clusterVisualization-method | Displays graphs of the differentially expressed clusters |
| connectivityProperties | Calculates average graph properties as a function of the node connectivity |
| connectivityProperties-method | Calculates average graph properties as a function of the node connectivity |
| DE | Get DE |
| DE-method | Get DE |
| DEsymbols | Dictionary Gene2Symbol |
| differentiallyExpressed | Identify which genes are differentially expressed |
| differentiallyExpressed-method | Identify which genes are differentially expressed |
| GPL570 | Dictionary Gene2Probe |
| GSE9988 | Data frame containing expression values |
| Hs700 | Ordered Homo sapiens proteins of combined score greater than or equal to 700 |
| Hs800 | Ordered Homo sapiens proteins of combined score greater than or equal to 800 |
| Hs900 | Ordered Homo sapiens proteins of combined score greater than or equal to 900 |
| HsBPTerms | Dictionary Gene2GO |
| Mm700 | Ordered Mus musculus proteins of combined score greater than or equal to 700 |
| Mm800 | Ordered Mus musculus proteins of combined score greater than or equal to 800 |
| Mm900 | Ordered Mus musculus proteins of combined score greater than or equal to 900 |
| orderingProperties | Calculates graph properties projected on the ordered proteins |
| orderingProperties-method | Calculates graph properties projected on the ordered proteins |
| radius | Radius |
| radius-method | Radius |
| radius<- | Radius |
| radius<--method | Radius |
| Rn700 | Ordered Rattus norvegicus proteins of combined score greater than or equal to 700 |
| Rn800 | Ordered Rattus norvegicus proteins of combined score greater than or equal to 800 |
| Rn900 | Ordered Rattus norvegicus proteins of combined score greater than or equal to 900 |
| Sc700 | Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 700 |
| Sc800 | Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 800 |
| Sc900 | Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 900 |
| Transcriptogram-class | Class Transcriptogram |
| transcriptogramPreprocess | Creates an object of class Transcriptogram |
| transcriptogramStep1 | Calculates the average of the expression values related to the same protein |
| transcriptogramStep1-method | Calculates the average of the expression values related to the same protein |
| transcriptogramStep2 | Calculates the average of the expression values using a sliding window |
| transcriptogramStep2-method | Calculates the average of the expression values using a sliding window |