Description

HiFive is a python package containing a set of tools for handling HiC and 5C data. This includes managing data from mapped reads, either in bam, mat, or raw formats. All stages use hdf5 dictionaries for fast access and minimal memory and storage usage. This package includes methods for normalizing data from either HiC or 5C experiments at the fragment-end, or fragment level resolution, respectively. Once normalized, data can be used for plotting, binning, or other statistical tests within the package very quickly. This package makes extensive use of the h5py and numpy packages. In addition, if mpi4py is installed, several methods are compatible with parallelization, including HiC normalization and heatmap generation.