BE3D: An Integrative Workflow for Structure–Function Analyses of Base-Editing Tiling Mutagenesis Data

This repository provides standardized datasets from five base-editing functional genomics studies, formatted specifically for BE3D benchmarking. Dataset Identifier Focus / Gene Target Primary Reference 1_LueDNMT3A2023 DNMT3A PMID: 36266353 2_PernerMEN12023 MEN1 PMID: 36922589 3_YeoKBTBD4–HDAC12025 KBTBD4, HDAC1 PMID: 39939761 4_HannaClinVarGenes2023 47 ClinVar study genes PMID: 33606977 5_LuSETDB1pathway2026 16 SETDB1 pathway genes PMID: Pending (TBA) Dataset Overview Format: Tab-separated values (.tsv) Data Schema: Gene: Target gene symbol. Mutation_type: Mutation classification of the base editing outcome. Mutation_list: Predicted base editing edits. sgRNA_score: Functional readout score. Preprocessing Pipeline: Standardized column names (Gene, Mutation_type, Mutation_list, and sgRNA_score) across all source datasets to ensure seamless compatibility with BE3D benchmarking frameworks.