standardgalactic / rna-scoop Goto Github PK

RNA Scoop is a tool to visualize isoforms in single cell transcriptomes. Through use of an interactive t-SNE plot, users are able to explore isoforms in a single-cell transcriptome dataset of thousands of cells.

Specifically, users are able to:

• View isoform structure
• Identify isoform expression levels within cells
• Compare isoform expression across clusters

Written by Maria Stephenson and Ka Ming Nip 📧

Dependency 📌

• Java SE Runtime Environment (JRE) 8

Installation 🔧

1. Download the binary tarball rnascoop_vX.X.X.tar.gz from the releases section
2. Extract the downloaded tarball with the command:

tar -zxf rnascoop_vX.X.X.tar.gz

RNA-Scoop can be run as java -jar /path/to/RNA-Scoop.jar ...

Implementation 📝

RNA-Scoop is written in Java with IntelliJ IDEA. It uses the following external libraries:

• T-SNE-Java
• Java UMAP
• JFreeChart (Future State Edition)
• JSON-Java
• ControlsFX