Changes in version 1.5.1: o Change on the differentiallyExpressed() method return: output now contains raw p-values. o Change on the clusterEnrichment() method return: output now contains raw p-values. o A section called "Frequently asked questions" has been added in the vignette. Changes in version 1.3.6: o Slot genesInTerm added to the Transcriptogram class. o Argument boundaryConditions from differentiallyExpressed(): default changed from FALSE to TRUE. o Argument onlyGenesInDE from clusterVisualization(): default changed from TRUE to FALSE. o Argument onlyGenesInDE from clusterEnrichment(): default changed from TRUE to FALSE. o Argument colors added to the differentiallyExpressed() method. o Argument colors added to the clusterVisualization() method. o Argument colors added to the enrichmentPlot() method. o Argument alpha added to the enrichmentPlot() method. Changes in version 1.3.4: o Argument universe from clusterEnrichment(): default changed from "all the proteins present in the transcriptogramS2 slot" to "all the proteins present in the ordering slot". Changes in version 1.3.3: o Change on the clusterEnrichment() method return. o Slots Protein2GO, and Terms added to the Transcriptogram class. o New methods: enrichmentPlot() and Terms(). Changes in version 1.3.1: o Argument boundaryConditions added to the differentiallyExpressed() method. o Slots Protein2Symbol, clusters, and pbc added to the Transcriptogram class. o Argument onlyGenesInDE added to the clusterVisualization() method. o Argument onlyGenesInDE added to the clusterEnrichment() method. Changes in version 1.1.18: o The differentiallyExpressed() method plot now uses the ggplot2 package and shows the number of clusters detected. Changes in version 1.1.11: o Argument title added to the differentiallyExpressed() method. Changes in version 1.1.7: o Argument trend added to the differentiallyExpressed() method to support limma-trend. Changes in version 1.1.6: o GPL570 dataset updated. Changes in version 1.1.3: o All species datasets (Homo sapiens, Mus musculus, Saccharomyces cerevisiae and Rattus norvegicus) were updated to obtain a better clustering. Changes in version 1.0.0: o Released at Bioconductor [2017-10-31].