The diffloop package contains a suite of tools and S4 data objects to efficiently facilitate the analysis of ChIA-PET datasets. Key features include differential loop calling, visualization of looping in regions, quality-control metrics, and principal component analysis across experiments.
Three classes mostly comprise the methodology in
loops is a basic structure that contains one or more ChIA-PET
loopfit links an
edgeR fit to a
and currently has little functionality except for generating another
loops object where per-loop summary statistics are added.
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