Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data

This repository contains input files from the synthetic, curated, and processed experimental single-cell gene expression datasets used in BEELINE. New in version 4:1) We are updating the configuration files and directory structure for the BEELINE v1.1 release. 2) PlotSyntheticNetworks.yaml and PlotCuratedNetworks.yaml can be used to recreate Figures 2 and 4, respectively, from the original paper. 3) This version will not work with versions of BEELINE before BEELINE v1.1. Use version 3 of this dataset if you are using code from before 2026/03/13.