Bi X, Ye W, Cheng X, Yang N, Wu X. vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data.
Bioinformatics 2024;
40:btae099. [PMID:
38485700 PMCID:
PMC10950478 DOI:
10.1093/bioinformatics/btae099]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/11/2024] [Indexed: 03/21/2024] Open
Abstract
MOTIVATION
Alternative polyadenylation (APA) is a widespread post-transcriptional regulatory mechanism across all eukaryotes. With the accumulation of genome-wide APA sites, especially those with single-cell resolution, it is imperative to develop easy-to-use visualization tools to guide APA analysis.
RESULTS
We developed an R package called vizAPA for visualizing APA dynamics from bulk and single-cell data. vizAPA implements unified data structures for APA data and genome annotations. vizAPA also enables identification of genes with differential APA usage across biological samples and/or cell types. vizAPA provides four unique modules for extensively visualizing APA dynamics across biological samples and at the single-cell level. vizAPA could serve as a plugin in many routine APA analysis pipelines to augment studies for APA dynamics.
AVAILABILITY AND IMPLEMENTATION
https://github.com/BMILAB/vizAPA.
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