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flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data

Szkop, KJ; Moss, DS; Nobeli, I; (2020) flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data. Bioinformatics 10.1093/bioinformatics/btaa854. (In press). Green open access

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Abstract

Motivation: We 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. 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 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.

Type: Article
Title: flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/bioinformatics/btaa854
Publisher version: https://doi.org/10.1093/bioinformatics/btaa854
Language: English
Additional information: This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology
URI: https://discovery.ucl.ac.uk/id/eprint/10117403
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