Qian Zhao
@qian613.bsky.social
We designed metaAPA to integrate the outputs of APA tools, which can extract high-confidence sites, supported by all methods, as well as putative sites supported by a subset of methods. We show that these high-confidence sites exhibit the expected biological sequence characteristics.
metaAPA: a tool for integration of PolyA site predictions from single-cell and spatial transcriptomics https://www.biorxiv.org/content/10.1101/2025.09.29.679268v1
October 2, 2025 at 1:11 PM
We designed metaAPA to integrate the outputs of APA tools, which can extract high-confidence sites, supported by all methods, as well as putative sites supported by a subset of methods. We show that these high-confidence sites exhibit the expected biological sequence characteristics.
We compared APA detection tools' performance in identification, quantification, and DE across single cell and spatial 3' tagging sequencing data using matched ONT data as ground truth. Our analysis of factors affecting performance offers guidance for biologists and insights for developing new tools.
Guidelines for alternative polyadenylation identification tools using single-cell and spatial transcriptomics data https://www.biorxiv.org/content/10.1101/2024.11.29.626111v1
Guidelines for alternative polyadenylation identification tools using single-cell and spatial transcriptomics data https://www.biorxiv.org/content/10.1101/2024.11.29.626111v1
Background: Many popular single-cell and spatial transcriptomics platforms exhibit 3' bias, making i
www.biorxiv.org
December 6, 2024 at 4:36 PM
We compared APA detection tools' performance in identification, quantification, and DE across single cell and spatial 3' tagging sequencing data using matched ONT data as ground truth. Our analysis of factors affecting performance offers guidance for biologists and insights for developing new tools.
Reposted by Qian Zhao
Guidelines for alternative polyadenylation identification tools using single-cell and spatial transcriptomics data https://www.biorxiv.org/content/10.1101/2024.11.29.626111v1
Guidelines for alternative polyadenylation identification tools using single-cell and spatial transcriptomics data https://www.biorxiv.org/content/10.1101/2024.11.29.626111v1
Background: Many popular single-cell and spatial transcriptomics platforms exhibit 3' bias, making i
www.biorxiv.org
December 4, 2024 at 10:46 PM
Guidelines for alternative polyadenylation identification tools using single-cell and spatial transcriptomics data https://www.biorxiv.org/content/10.1101/2024.11.29.626111v1