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VizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data.

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.

SUBMITTER: Bi X

PROVIDER: S-EPMC10950478 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature

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vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data.

Bi Xingyu X Ye Wenbin W Cheng Xin X Yang Ning N Wu Xiaohui X

Bioinformatics (Oxford, England) 20240301 3

<h4>Motivation</h4>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.<h4>Results</h4>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 annotat ...[more]

PMID: 38485700

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