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).
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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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