Figure 1

Transcriptomic analysis workflows using GIANT Galaxy tools. The general steps of the workflows are indicated on the left. Two workflows depending on the initial raw data are represented, both starting from the design definition (at the center bottom) to generic data mining analyses (purple dashed area at the top). Specific steps from quality check to differential analysis are indicated for microarray (left, green dashed area) and RNA-seq (right, yellow dashed area). Steps in which GIANT tools can be used are coloured in red, specific RNA-seq steps with available Galaxy tools are coloured in blue. Arrows \(1_m\)-\(5_m\) and \(1_r\)-\(6_r\) indicate the tools which should be used in consecutive steps for microarray and RNA-seq data analysis, respectively. Note that running the Quality Check tool both before and after data normalization is recommended (*marked).