flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data.
Bioinformatics
; 37(10): 1461-1464, 2021 06 16.
Article
em En
| MEDLINE
| ID: mdl-33051680
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. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Poliadenilação
Idioma:
En
Ano de publicação:
2021
Tipo de documento:
Article