Your browser doesn't support javascript.
loading
scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data.
Ye, Congting; Zhou, Qian; Wu, Xiaohui; Yu, Chen; Ji, Guoli; Saban, Daniel R; Li, Qingshun Q.
Afiliação
  • Ye C; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.
  • Zhou Q; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.
  • Wu X; Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.
  • Yu C; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China.
  • Ji G; Department of Ophthalmology, Duke University, Durham, NC 27710, USA.
  • Saban DR; Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.
  • Li QQ; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China.
Bioinformatics ; 36(4): 1262-1264, 2020 02 15.
Article em En | MEDLINE | ID: mdl-31557285
ABSTRACT
MOTIVATION Alternative polyadenylation (APA) plays a key post-transcriptional regulatory role in mRNA stability and functions in eukaryotes. Single cell RNA-seq (scRNA-seq) is a powerful tool to discover cellular heterogeneity at gene expression level. Given 3' enriched strategy in library construction, the most commonly used scRNA-seq protocol-10× Genomics enables us to improve the study resolution of APA to the single cell level. However, currently there is no computational tool available for investigating APA profiles from scRNA-seq data.

RESULTS:

Here, we present a package scDAPA for detecting and visualizing dynamic APA from scRNA-seq data. Taking bam/sam files and cell cluster labels as inputs, scDAPA detects APA dynamics using a histogram-based method and the Wilcoxon rank-sum test, and visualizes candidate genes with dynamic APA. Benchmarking results demonstrated that scDAPA can effectively identify genes with dynamic APA among different cell groups from scRNA-seq data. AVAILABILITY AND IMPLEMENTATION The scDAPA package is implemented in Shell and R, and is freely available at https//scdapa.sourceforge.io. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Assuntos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Poliadenilação / RNA-Seq Tipo de estudo: Diagnostic_studies Idioma: En Revista: Bioinformatics Assunto da revista: INFORMATICA MEDICA Ano de publicação: 2020 Tipo de documento: Article País de afiliação: China

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Poliadenilação / RNA-Seq Tipo de estudo: Diagnostic_studies Idioma: En Revista: Bioinformatics Assunto da revista: INFORMATICA MEDICA Ano de publicação: 2020 Tipo de documento: Article País de afiliação: China