stAPAminer Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies
Introduction
stAPAminer first identifies poly(A) sites from spatial RNA-seq and then qantifies APA site usages in individual spots. Particularly, we imputes APA site usages with gene expression profiles to avoid high sparseness. Using stAPAminer, we can detect poly(A) sites from genes in MOB and found genes with spatial patterns of APA usage. Genes with spatial patterns of APA usage are predicted compared to genes with spatial patterns of gene expression.
stAPAminer is available at https://github.com/BMILAB/stAPAminer.
Publications
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Credits
- Zhu Sheng 1468833954@qq.com Investigator
School of Aerospace engineering, Xiamen University, China
Community Ratings
Usability | Efficiency | Reliability | Rated By |
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Accession | BT007320 |
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Tool Type | Toolkit |
Category | Polyadenylation data |
Platforms | Linux/Unix, Windows |
Technologies | R |
User Interface | Desktop GUI |
Input Data | FASTA |
Latest Release | v1.0 (August 3, 2022) |
Download Count | 1062 |
Country/Region | China |
Submitted By | Zhu Sheng |
This work was supported by the National Natural Science Foundation of China (Grant No. 61673323 to X.W., 61573296 to G.J. and 81901287 to S.X.) and Suzhou City People’s Livelihood Science and Technology Project (SYS2020086 to S.X.).