Galaxy Scatterplot visualization of transcript differential expression from the Tophat-Cufflinks pipeline for an experiment measuring expression of ~2,500 transcripts in brain and adrenal tissue from the BodyMap 2.0 dataset (EBI accession E-MTAB-513). Clicking on the visualize icon for the dataset (top) opens up the scatter plot visualization directly in Galaxy’s analysis workspace (bottom). Columns for control and treatment FPKM are visualized, and gene name is used for labeling. The scatterplot shows that most transcripts are expressed at low levels in both conditions. However, a small number of transcripts are highly expressed in either the control, treatment, or both. Hovering over a data points shows its label and data; a transcript for the AES gene shows decreased expression in the treatment condition as compared to the control condition.