Create script annotate_with_file with MooseX::App
Migrate script annotate_with_deletions to MooseX::App
Replace dev.off with graphics.off in R scripts

graphics.off suppresses return value "null device 1"
Create PlotApp for creating plots
Migrate script plot_distribution_on_genic_elements to PlotApp (MooseX::App)
Migrate script plot_distribution_on_introns_exons to PlotApp (MooseX::App)
Migrate script plot_genomic_distribution to PlotApp (MooseX::App)
Migrate script plot_libraries_relative_read_density to PlotApp (MooseX::App)
Add plotting functionality and option in all scripts that support it
Use Statistics::R for plots instead of R scripts