Fig. 1

Overview of a deltaRpkm workflow. Black arrows indicate the main pipeline; dotted arrows show an alternative route with STAR. The package is written in R and takes as input a canonical coverage table, plus the design information given by the user as a metadata table. The strength of deltaRpkm relies on bypassing the tedious assembly and annotation steps typical of comparative genomics. Instead, deltaRpkm uses a basic gene read counts table (based on the mapping against a reference genome) to compute inter-group differential RPKM values per gene and outputs a list of candidate genes as present in the samples of the reference genome group (and absent from the comparison group)