A ShinyApp for scRNA-seq analysis

Published: 4 September 2024| Version 1 | DOI: 10.17632/t38rw5fg82.1
Contributors:
Ziyi Wang, Mitsuaki Ono

Description

This R Shiny software provides a simple interactive graphical user interface for exploring scRNAseq data, assessing the biological relevance of clustering results, and performing trajectory analysis with STREAM and the scVelco algorithm.

Files

Steps to reproduce

To run this R Shiny software, you have to run an R script named "00.R_PackageSetting.R" under the folder titled "GlobalEnvironment" to install the required dependencies. The Python codes for RNA velocity (scVelo) and Single-cell Trajectory Reconstruction Exploration And Mapping (STREAM) analysis are available under "00.pySource." You can also run these trajectory analyses inside this R Shiny software through the menu named "Trajectory Inference." Re-analysis of two example datasets (GSE261806 and GSE155928) are available in the "ExampleData" folder. A preview of this software is available in the below link: https://s3.okayama-u-bsg.org?appName=GSE261806

Institutions

Okayama Daigaku

Categories

Bioinformatics Software, Single-Cell RNA Sequencing

Licence