All datasets were updated to match data from STRINGdb release 11.
Change on the differentiallyExpressed() method return: output now contains raw p-values.
Change on the clusterEnrichment() method return: output now contains raw p-values.
A section called "Frequently asked questions" has been added in the vignette.
Slot genesInTerm added to the Transcriptogram class.
Argument boundaryConditions from differentiallyExpressed(): default changed from FALSE to TRUE.
Argument onlyGenesInDE from clusterVisualization(): default changed from TRUE to FALSE.
Argument onlyGenesInDE from clusterEnrichment(): default changed from TRUE to FALSE.
Argument colors added to the differentiallyExpressed() method.
Argument colors added to the clusterVisualization() method.
Argument colors added to the enrichmentPlot() method.
Argument alpha added to the enrichmentPlot() method.
Argument universe from clusterEnrichment(): default changed from "all the proteins present in the transcriptogramS2 slot" to "all the proteins present in the ordering slot".
Change on the clusterEnrichment() method return.
Slots Protein2GO, and Terms added to the Transcriptogram class.
New methods: enrichmentPlot() and Terms().
Argument boundaryConditions added to the differentiallyExpressed() method.
Slots Protein2Symbol, clusters, and pbc added to the Transcriptogram class.
Argument onlyGenesInDE added to the clusterVisualization() method.
Argument onlyGenesInDE added to the clusterEnrichment() method.
The differentiallyExpressed() method plot now uses the ggplot2 package and shows the number of clusters detected.
Argument title added to the differentiallyExpressed() method.
Argument trend added to the differentiallyExpressed() method to support limma-trend.
GPL570 dataset updated.
All species datasets (Homo sapiens, Mus musculus, Saccharomyces cerevisiae and Rattus norvegicus) were updated to obtain a better clustering.
Released at Bioconductor [2017-10-31].