BEELINE V1.0

BEELINE version 1.0 contains source code used in the Nature Methods version of the BEELINE paper. This release includes:

• Shell scripts for setting up BEELINE
• Dockerized versions of 12 GRN inference algorithms tested in BEELINE paper
• BLRun, a module for running GRN inference algorithms
• BLEval, a module that provides easy-to-use tools for evaluating GRN reconstructions
• BLPlot, source code used for generating summary plots in the BEELINE paper

BLEval module contains source code used for computing area under the ROC curve, area under the precision-recall curve, early precision, early precision for signed edges, various stability measures, network motifs, shortest path analysis, and Borda aggregation. This version excludes source code for parameter estimation, which will be integrated into the BLRun module in a future release. Please note that the code for parameter estimation is currently under the parameter-search branch. The documentation for BEELINE is available at: https://murali-group.github.io/Beeline/BEELINE.html. The input datasets used in BEELINE are available at: https://doi.org/10.5281/zenodo.3378975.