ArticleBioinformatics (Oxford, England)2021
flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Benchmarking of methods that identify alternative polyadenylation events in single-/multiple-polyadenylation site genes.NAR genomics and bioinformatics · 2025Review
- Polygenic risk for schizophrenia converges on alternative polyadenylation as molecular mechanism underlying synaptic impairment.bioRxiv : the preprint server for biology · 2024Article
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3 authors.
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Abstract
motivationWe present flexible Modeling of Alternative PolyAdenylation (flexiMAP), a new beta-regression-based method implemented in R, for discovering differential alternative polyadenylation events in standard RNA-seq data.
resultsWe show, using both simulated and real data, that flexiMAP exhibits a good balance between specificity and sensitivity and compares favourably to existing methods, especially at low fold changes. In addition, the tests on simulated data reveal some hitherto unrecognized caveats of existing methods. Importantly, flexiMAP allows modeling of multiple known covariates that often confound the results of RNA-seq data analysis. AVAILABILITY AND IMPLEMENTATION: The flexiMAP R package is available at: https://github.com/kszkop/flexiMAP. Scripts and data to reproduce the analysis in this paper are available at: https://doi.org/10.5281/zenodo.3689788. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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