{"doi":"10.1101/2021.11.01.466854","title":"Exploration and analysis of R-loop mapping data with <i>RLBase</i>","abstract":"Abstract R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA during nascent transcription. In 2012, Ginno et al. introduced the first R-loop mapping method, DNA:RNA immunoprecipitation (DRIP) sequencing. Since that time, dozens of studies have implemented R-loop mapping and new high-resolution techniques have been developed. The resulting datasets have tremendous potential to reveal the causes and consequences of R-loops genome-wide. However, poor quality and variability between mapping approaches pose serious barriers to the meta-analysis of these data. In our recent work, we reprocessed 693 R-loop mapping samples, devising new quality methods, defining a set of high-confidence mapping samples, and then deriving R-loop regions, consensus sites of R-loop formation. This analysis yielded the largest R-loop data resource to date along with novel computational approaches for R-loop mapping analysis. Now, we introduce RLBase , an innovative web server which builds upon those data and software by providing users with the capability to (1) explore hundreds of public R-loop mapping datasets, (2) explore consensus R-loop regions, (3) analyze user-supplied datasets to generate an HTML quality report, and (4) download all the processed data for the 693 samples we previously reprocessed and standardized. In addition to RLBase , we also describe the other software which, along with RLBase , provides a computational framework for R-loop bioinformatics. RLBase , and the rest of these software (termed “RLSuite”), are provided freely under an MIT license and made publicly available: https://gccri.bishop-lab.uthscsa.edu/rlsuite/ . RLBase is directly accessible via the following URL: https://gccri.bishop-lab.uthscsa.edu/rlbase/ .","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":221988,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8085,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":292965,"name":"Daniel Montemayor","orcid":"0000-0001-8702-5646","position":1,"is_corresponding":false},{"id":822613,"name":"J. Li","orcid":"0000-0002-8909-9048","position":2,"is_corresponding":false},{"id":813345,"name":"Simon A. Levy","orcid":"0000-0002-4623-5716","position":3,"is_corresponding":false},{"id":823153,"name":"Roshan Pawar","orcid":null,"position":4,"is_corresponding":false},{"id":290916,"name":"Stella R. Hartono","orcid":"0000-0001-6234-3445","position":5,"is_corresponding":false},{"id":292969,"name":"Kumar Sharma","orcid":"0000-0002-7550-8525","position":6,"is_corresponding":false},{"id":79790,"name":"Bess Frost","orcid":"0000-0002-1212-8138","position":7,"is_corresponding":false},{"id":247517,"name":"Frédéric Chédin","orcid":"0000-0002-1306-5335","position":8,"is_corresponding":false},{"id":97807,"name":"Alexander J.R. Bishop","orcid":"0000-0002-5742-4387","position":9,"is_corresponding":false},{"id":310418,"name":"Henry E. Miller","orcid":"0000-0003-3756-3918","position":0,"is_corresponding":true}],"reference_count":45,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-18T23:53:59.302331Z","pmid":null,"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":[]}