An R package for identifying differential features from chromatin capture confirmation experiments.
Raw FASTQ read files can be preprocessed with the
(https://github.com/dphansti/mango) software, an
R package that relies
MACS2 to align reads,
call anchor peaks, and summarize PETs per sample in the ChIA-PET experiment.
Sample analysis with diffloop
Check out the vignette for a working example on quality control, visualization, association, and annotation.
Check out DNAlandscapeR for an R/Shiny environment to visualize topology data interactively.
Caleb Lareau is the primary maintainer/developer of diffloop.