BEAR-GRN: Benchmarking, Evaluation and Assessment Resource for GRNs

This directory contains the data required to reproduce the benchmarking results as reported in BEAR-GRN. This data is also required for benchmarking new GRN inference methods utilizing multiomics. INFERRED.GRNS - contains the inferred GRNs from Eight GRN inference methods for eight dataset used in BEAR-GRN GROUND.TRUTHS - contain the ground truth filtered for expressed genes in each dataset STABILITY_GRNS - contain the inferred GRNs from mESC subsamples created for stability measument for Eight GRN inference methods INPUT.DATA - Contains processed multiomic data used for GRN inference (Gene by Cell and Peak by Cell matrix) INPUT.DATA.STABILITY - Contains rds file of subsampled scRNA and scATAC data and a script that can be used to generate matrix and create subsamples directories using RDS files GENOME_AND_ANNOTATION - contains the genome, annotation, motif annotation, PWM files used by these inference algorithms for reproducibility