{"doi":"10.1093/bioinformatics/btaf590","title":"PathwayVote: an R package for robust pathway enrichment analysis for DNA methylation data using a consensus-based voting framework","abstract":"MOTIVATION: Pathway enrichment analysis is commonly used to interpret epigenomewide association studies, yet conventional methods often rely on arbitrary thresholds and simplified CpG-gene mappings, making them sensitive to analytical choices and unable to fully leverage CpG-gene relationships Recent advances in expression quantitative trait methylation (eQTM) studies offer a rich resource to refine these mappings, but are rarely utilized in DNA methylation enrichment pipelines. RESULTS: We developed PathwayVote, an R package that implements a voting-based consensus approach and leverages eQTM data to identify robustly enriched pathways. PathwayVote reduces dependence on arbitrary cutoffs and improves sensitivity and reproducibility of enrichment results. AVAILABILITY AND IMPLEMENTATION: PathwayVote is freely available on GitHub (https://github.com/YinanZheng/PathwayVote) under the GPL-3 license and CRAN: https://CRAN.R-project.org/package=PathwayVote. The version of the code corresponding to this manuscript has been archived on Zenodo (https://doi.org/10.5281/zenodo.17209507).","journal":"Bioinformatics","year":2025,"id":579290,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9528,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":628912,"name":"Feng Gao","orcid":"0000-0002-1641-2101","position":1,"is_corresponding":false},{"id":218546,"name":"Lifang Hou","orcid":"0000-0003-4877-0031","position":2,"is_corresponding":false},{"id":291153,"name":"Yinan Zheng","orcid":"0000-0002-2006-7320","position":0,"is_corresponding":true}],"reference_count":10,"raw_metadata":null,"created_at":"2026-07-19T02:58:30.282164Z","pmid":"41143682","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}