a number of functions to facilitate more in-depth or custom analysis in R: – Do more nuanced, custom filtering of hits by score and coverage – Annotate any motif of interest in both the gff/contexts and the genome reference – Plot the score vs. coverage distribution by base – Examine the distribution of score, coverage, IPD Ratio or other factors for any motif of interest, both modified or unmodified – Visualize your results using circos • Example data and R functions can be found online: – https://github.com/PacificBiosciences/Bioinformatics- Training/tree/master/basemods – http://pacb.com/bmd/ (basemod data sets at PacBio) – https://github.com/PacificBiosciences/R-kinetics (github R Kinetics package) 4