The R-loop, a three-stranded nucleic acid structure composed of an RNA:DNA hybrid and a displaced single-stranded DNA, plays versatile roles in many physiological and pathological processes. We therefore present R-loopBase to address these pressing issues (Lin et al., Nucleic Acids Res., 2022). Species- and cell type-resolved R-loop zones are computed with both categorical and quantitative confidence scores (Search, Help and Download). R-loop regulators in humans and several model organisms were manually curated from the literature, and their targeted R-loops were deduced from functional genomics data (Regulator and Download). Billions of functional annotation entries have been generated and can be visualized in a well-annotated genomic context through a local genome browser (Browser) and explored using analytical tools (DeepER and R-loopReGSEA). Your contribution (Regulator Updating System) and suggestions are welcome (Contact).

• Species- and cell type-resolved quantitative map of R-loop regions are provided.
• More R-loop mapping datasets have been analyzed and archived, including 358 in human, 71 in mouse, 46 in fruit fly, and 23 in yeast.
• R-loop regulators have been expanded to 1,709 in human, 76 in mouse, 10 in fruit fly, 77 in yeast (saccharomyces cerevisiae) and 23 in Escherichia coli.
• Online of DeepER, a deep learning enhanced R-loop prediction tool (Hu et al., iScience, 2023).
• Online of R-loopReGSEA for R-loop regulator enrichment analysis.
• Online of a user-friendly download portal.
• More species are supported by R-loopBase genome browser

• A categorical (confidence-based) map of human R-loops is provided.
• 1,185 R-loop regulators in human, 24 in mouse, 63 in yeast (saccharomyces cerevisiae) and 21 in Escherichia coli have been manually curated from literature.
• 118 R-loop mapping datasets have been analyzed and archived.
• Build-up of R-loopBase genome browser for human.