◌ Select an experiment, then a chromosome, to explore its contact map and 3D model.
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About PHi-D
Welcome to PHi-D — an interactive home for exploring and sharing analyzed Hi-C genome data. It is the next-generation companion to RIKEN's phid.riken.jp site, built for researchers who want to see the 3D genome, not just download a file.
For each dataset you can explore an interactive contact map — the experimental Hi-C data and the PHi-C2 polymer-model fit shown side by side — together with an animated, colorable 3D chromosome model, the MSD and loss-tangent maps that describe how the genome moves and flexes, and a 1D genome view. The panels are linked: zoom or hover one and the others follow the same genomic position.
The science comes from PHi-C2 (Shinkai et al.), a polymer-physics method that reads a Hi-C contact matrix as the dynamic 3D state of the genome. The heatmaps render directly from the full-precision analyzed data — stored in Zarr, a community-standard scientific array format — so what you see on screen is the real science itself, with fast zoom, smooth panning, and instant recoloring.
PHi-D is built to last: everything is pre-computed offline and served as plain static files, with no framework standing between you and the data — a simple, durable foundation meant to stay useful for many years.
Data source: 4DN · Analysis: PHi-C2 · Contact: phid-support@ml.riken.jp