- deeptools computematrix
This tool calculates scores per genome regions and prepares an intermediate file that can be used with plotHeatmap and plotProfiles
- deeptools plotprofile
This tool creates a profile plot for scores over sets of genomic regions
- deeptools plotfingerprint
This quality control will most likely be of interest for you if you are dealing with ChIP-seq samples as a pressing question in ChIP-seq experiments is Did my ChIP work?