ArticleBMC bioinformatics2023
FLARE: a fast and flexible workflow for identifying RNA editing foci.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- ADARs mediate distinct RNA editing activity and gene regulation in theRNA (New York, N.Y.) · 2026Article
- ADARs mediate distinct RNA editing activity and gene regulation in thebioRxiv : the preprint server for biology · 2025Article
- Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues.Nature methods · 2025Article
- ncRNA Editing: Functional Characterization and Computational Resources.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Identification of RBP binding sites using RNA deaminases.Methods in enzymology · 2025Article
- LoDEI: a robust and sensitive tool to detect transcriptome-wide differential A-to-I editing in RNA-seq data.Nature communications · 2024Article
- High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues.Nature communications · 2024Article
- Article
- Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.Nature communications · 2024Article
- The role of ADAR1 through and beyond its editing activity in cancer.Cell communication and signaling : CCS · 2024Review
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Authors and funding
4 authors.
Funding
Abstract
backgroundFusion of RNA-binding proteins (RBPs) to RNA base-editing enzymes (such as APOBEC1 or ADAR) has emerged as a powerful tool for the discovery of RBP binding sites. However, current methods that analyze sequencing data from RNA-base editing experiments are vulnerable to false positives due to off-target editing, genetic variation and sequencing errors.
resultsWe present FLagging Areas of RNA-editing Enrichment (FLARE), a Snakemake-based pipeline that builds on the outputs of the SAILOR edit site discovery tool to identify regions statistically enriched for RNA editing. FLARE can be configured to analyze any type of RNA editing, including C to U and A to I. We applied FLARE to C-to-U editing data from a RBFOX2-APOBEC1 STAMP experiment, to show that our approach attains high specificity for detecting RBFOX2 binding sites. We also applied FLARE to detect regions of exogenously introduced as well as endogenous A-to-I editing.
conclusionsFLARE is a fast and flexible workflow that identifies significantly edited regions from RNA-seq data. The FLARE codebase is available at https://github.com/YeoLab/FLARE .
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