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| RTools4TB_1.1.4-package | The RTools4TB package: data mining of public microarray data through connections to the TranscriptomeBrowser database. |
| annotationList | The keywords used to get information about functional enrichment of transcriptional signatures. |
| clusterEisen | Performs system call to the Cluster 3.0 program. |
| colorScale | Calibration bar for color images |
| createGraph4BioC | Creates a graph based on a request to the TrancriptomeBrowser database. |
| createSignatures4TB | Creates a set of transcriptional signatures from a microarray dataset. |
| DBF | Density-Based Filtering. |
| DBFMCL | The "Density Based Filtering and Markov CLustering" algorithm (DBF-MCL). |
| DBFMCLresult | Class to store DBFMCL results. |
| DBFMCLresult-class | Class to store DBFMCL results. |
| doNormalScore | Normal score transformation of a matrix. |
| doRankTransformation | Rank transformation of a matrix. |
| getData4DBFMCL | Fetch an expression matrix from a file or an ExpressionSet object |
| getExpressionMatrix | A function to fetch an expression matrix from the TranscriptomeBrowser database. |
| getSignatures | A function to retrieve transcriptional signature IDs from the TranscriptomeBrowser database (TBrowserDB). |
| getTBInfo | Get information about an experiment or a platform. |
| heatmapFromCDT | Reads a "cdt" file containing a set of transcriptional signatures and produces heatmaps. |
| matplotProfiles | An internal plotting function based on the matplot function. |
| MCL | Invokes the Markov CLustering algorithm (MCL). |
| plotGeneExpProfiles | Visualization of transcriptional signature profiles. |
| RTools4TB | The RTools4TB package: data mining of public microarray data through connections to the TranscriptomeBrowser database. |
| show,DBFMCLresult-method | Class to store DBFMCL results. |
| writeDBFMCLresult | Writes the results of DBFMCL function onto disk. |