Fig. 1
From: GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
Overview of the GeneTonic workflow. Four elements are required to optimally use the functionality of GeneTonic (top section): dds, a DESeqDataSet, with the information related to the expression values; res_de, a DESeqResults object, storing the results of the differential expression analysis; res_enrich, a data frame with the result from the enrichment analysis; annotation_obj, a data frame containing different sets of matched identifiers for the features of interest. These can be combined into a GeneTonicList object (middle section), which can be directly fed to GeneTonic and its functions, enabling (bottom section) interactive exploration and a variety of visualizations on the geneset enrichment results, both exploited to generate an integrated HTML report of the provided data