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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 ๐Ÿ“ง


Disclaimer โš ๏ธ

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.

Dependency ๐Ÿ“Œ

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

Installation ๐Ÿ”ง

  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 simple as:

java -jar /path/to/RNA-Scoop.jar ...

Tutorial ๐Ÿ”

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.

RNA-Scoop @ BioVis ISMB 2020

Setting max heap space in Java ๐Ÿ’พ

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.

Implementation ๐Ÿ“

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

Citing RNA-Scoop ๐Ÿ“œ

If you use RNA-Scoop in your work, please cite our publication:

Maria Stephenson, Ka Ming Nip, Saber HafezQorani, Kristina K Gagalova, Chen Yang, Renรฉ 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