Szkop, Krzysztof J. and Moss, David S. and Nobeli, Irene (2021) flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data. Bioinformatics 37 (10), pp. 1461-1464. ISSN 1367-4803.
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Abstract
Motivation: We present flexible Modeling of Alternative PolyAdenylation (flexiMAP), a newbeta-regression-based method implemented in R, for discovering differential alternative polyadenylation events in standard RNA-seq data. Results: We 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 flexiMAPR 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.
Metadata
| Item Type: | Article |
|---|---|
| School: | Birkbeck Faculties and Schools > Faculty of Science > School of Natural Sciences |
| Depositing User: | Irene Nobeli |
| Date Deposited: | 11 Nov 2020 11:52 |
| Last Modified: | 02 Aug 2023 18:04 |
| URI: | https://eprints.bbk.ac.uk/id/eprint/40971 |
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