scHiCTools: a computational toolbox for analyzing single cell Hi-C data

Here, we present an open source computational toolbox, scHiCTools, which provides three commonly used methods for smoothing scHi-C data (linear convolution, random walk, and network enhancing) and three projection methods for embedding single cells into a lower dimensional Euclidean space (fastHiCRep, Selfish, and InnerProduct). We benchmark the embedding performance and run time of these methods on a recent scHi-C datasets, and provide some suggestions for practice use.