ArticleBioinformatics (Oxford, England)2020
scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- miRNA regulation in brain tissue space: the 3'UTR perspective.RNA (New York, N.Y.) · 2026Review
- TREM2 in age-related macular degeneration: a microglia-centered perspective in the retinal myeloid landscape.Frontiers in ophthalmology · 2026Review
- Single-nucleus transcriptome atlas of orbitofrontal cortex in ALS with a deep learning-based decoding of alternative polyadenylation mechanisms.Cell genomics · 2025Article
- Alternative cleavage and polyadenylation: key regulatory mechanisms in health and disease.RNA biology · 2025Review
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data.Bioinformatics (Oxford, England) · 2024Article
- Microglia at sites of atrophy restrict the progression of retinal degeneration via galectin-3 and Trem2.The Journal of experimental medicine · 2024Article
- Dynamics of alternative polyadenylation in single root cells ofFrontiers in plant science · 2024Article
- Infernape uncovers cell type-specific and spatially resolved alternative polyadenylation in the brain.Genome research · 2023Article
- Stress responses of plants through transcriptome plasticity by mRNA alternative polyadenylation.Molecular horticulture · 2023Review
- stAPAminer: Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies.Genomics, proteomics & bioinformatics · 2023Article
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq.Genome biology · 2022Article
- scAPAmod: Profiling Alternative Polyadenylation Modalities in Single Cells from Single-Cell RNA-Seq Data.International journal of molecular sciences · 2022Article
- scMAPA: Identification of cell-type-specific alternative polyadenylation in complex tissues.GigaScience · 2022Article
- Review
- Shortening of 3' UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism.RNA (New York, N.Y.) · 2021Article
- Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression.Genome research · 2021Article
- The Detection and Bioinformatic Analysis of Alternative 3International journal of molecular sciences · 2021Review
- Alternative polyadenylation: methods, mechanism, function, and role in cancer.Journal of experimental & clinical cancer research : CR · 2021Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
motivationAlternative 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.
resultsHere, 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.