SCOUTS is a tool that quickly finds outliers in your single-cell data, generating information about your cell population organized by markers. It is designed to analyse mass cytometry (CyToF) and single-cell RNA sequencing data (scRNASeq).
Many single-cell analytical pipelines require some level of programming knowledge in order to be used. While some great tools for languages like R, Python and Julia have been developed, the entry-level barrier of programming is still intimidating for many scientists starting on the field of singe-cell analysis. With this in mind, we developed SCOUTS to simplify this process. Through a desktop application, the user is able to choose the parameters for the outlier selection, and leave the hard work of programmatically subsetting the data to SCOUTS.
As a showcase of how to interpret and explore the data generated by SCOUTS, we also developed SCOUTS-violins, a secondary desktop application which displays the outlier populations identified by SCOUTS as violin plots.
SCOUTS is available as a:
- Python package from PyPI - install with
pip - Conda package - install with
conda - GitHub repository - download/clone the repository
- binary release (experimental)
Full installation instructions are found here.
Binary releases are found here. Keep in mind that these are experimental, and may not work properly on your system. In this case, we recommend following another installation method.
For any installation option (other than the binary release), SCOUTS requires Python >= 3.6.
The scouts package include two user interfaces:
- SCOUTS: used to select outliers in a population of single-cells. Here's a quick rundown of how to use SCOUTS.
- SCOUTS-violins (optional): used to visually inspect outliers selected by SCOUTS. Here's a quick rundown of how to use SCOUTS-violins.
Read the full documentation here.
Frequently asked questions can be found here.
If you use SCOUTS, please cite us.
Juliano Faccioni - Programming and GUI development
Giovana Onzi - Concept and testing
This project is licensed under the MIT License.
Scientific counselling
- Prof. Dr. Guido Lenz
Funding
- CAPES/CNPq
- NIH