Glossary

• HDF5 is a general purpose binary container format for large scientific datasets.

• h5py is a Python library providing low-level bindings to the libhdf5 C-library and a high-level, numpy-aware API to interact with HDF5 files on disk.

• The cooler data model is a flexible sparse data model for Hi-C and other genomically-labeled arrays.

• The cooler schema describes an implementation of the cooler data model using HDF5 as the underlying storage layer.

• Cooler files store one or more cooler data collections, each representing a genomically-labeled sparse array.

• Single-resolution cooler files are conventionally given the extension .cool. Multi-resolution files are usually suffixed .mcool.

• The cooler Python package provides an API to create cooler files and to interact with them both as data frames and sparse matrices.

• A genomic pairs list provides pointwise 2-tuples of single-bp genomic locations. In Hi-C this is also called a contact list.

• A genomic matrix, 2D array or heatmap assigns unique quantitative values to pairs of genomic intervals taken from a bin segmentation of a genome assembly. In Hi-C, a contact matrix is obtained by aggregating pairs.