Fig. 2

Selected screenshots of the ideal application. a Data Setup panel, after uploading the expression matrix and experimental design information, here displayed with the macrophage dataset illustrated as use case in Additional file 2. The setup steps appear consecutively once the required input elements and information are provided by the user. b Overview of the Summary Plots panel, with an MA plot displaying expression change (as \(\hbox {log}_{2}\) Fold Change) versus average expression level. Upon interaction via brushing, a zoomed plot appears, where features are labeled to facilitate further exploration, e.g. by displaying expression plots and information fetched from the NCBI Entrez database. c Results from the Functional Analysis panel, with an interactive table for the enriched Biological Processes. When clicking on a row of interest, a signature heatmap is shown to better show the behavior of the features annotated to the particular Gene Ontology term. d The Report Editor panel, accessed after computing all required objects (as shown by the green value boxes in the upper part of the subfigure), contains a text editor which displays the default comprehensive template provided with the package - which can additionally be edited by the user. In the framed content, a screenshot of the rendered report is included, e.g. with an annotated MA plot highlighting a set of specified genes