interactive visualization of single-cell transcriptomes
RNA Scoop is a tool to visualize isoforms in single cell transcriptomes. Through use of an interactive cell cluster 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 📧
RNA-Scoop is designed to work with data produced from single-cell protocols that supports transcript isoform level analysis. In other words, 3' end capture protocols (such as 10x Genomics or Drop-Seq) designed for measuring gene expression in single cells are NOT supported. Additionally, while the tool provides does provide fold-change values for isoforms, and a way to filter for different isoform expression patterns, it is primarily a visualization tool. One should use other tools specifically made for tasks like differential isoform expression analysis for more precise calculations.
- Java SE Runtime Environment (JRE) 8
- This is not the same as OpenJDK!
Alternatively, you can create a dedicated conda environment to install JRE8:
conda create -n jre-8-env -c cyclus java-jre -y
Please note that the above command does not install RNA-Scoop in conda!
To activate this conda environment, use
conda activate jre-8-env
You can run RNA-Scoop within this conda environment if you already have the RNA-Scoop JAR file. See the next section for more details.
To deactivate the active conda environment, use
conda deactivate
- Download the binary tarball
rnascoop_vX.X.X.tar.gzfrom the releases section - Extract the downloaded tarball with the command:
tar -zxf rnascoop_vX.X.X.tar.gz
RNA-Scoop can be run as simple as:
java -jar /path/to/RNA-Scoop.jar ...
Consult our wiki pages for an introduction to highlight features in RNA-Scoop.
Watch Maria's 8-minute conference talk at the BioVis COSI at ISMB 2020.
The memory required for RNA-Scoop depends of the dimension (rows, columns) of the input expression matrix. If a memory error is encountered while running RNA-Scoop (i.e. java.lang.OutOfMemoryError: Java heap space), then the max heap space in Java needs to be increased, e.g.
java -Xmx16g -jar /path/to/RNA-Scoop.jar ...
This limits the maximum Java heap to 16 GB with the -Xmx option. See documentation for other JVM options.
RNA-Scoop is written in Java with IntelliJ IDEA. It uses the following external libraries:
If you use RNA-Scoop in your work, please cite our publication:
Maria Stephenson, Ka Ming Nip, Saber HafezQorani, Kristina K Gagalova, Chen Yang, René L Warren, Inanc Birol. RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes. NAR Genomics and Bioinformatics, Volume 3, Issue 4, December 2021, lqab105, https://doi.org/10.1093/nargab/lqab105