This repository contains the source code for MaCroDNA (Matching Cross-Domain Nucleic Acids) described in the paper "Accurate integration of single-cell DNA and RNA for analyzing intratumor heterogeneity using MaCroDNA" along with the scripts necessary for reproducing the results and the figures presented in the paper. MaCroDNA is a tool for integration of single-cell RNA and DNA data sequenced by high-throughput single-cell sequencing technologies. MaCroDNA uses maximum weighted bipartite matching of per-gene read counts from single-cell copy number and gene expression data to find the correspondence between the single cells from the two modalities.