scRAFIKI - Single-cell RNA-seq Atlas Framework for Integration and Key Insights

Note

This tool has recently been renamed. Previously, it was called SIMBA.

scRAFIKI is a pipeline designed to integrate single-cell RNA-seq datasets to generate atlases. It incorporates several integration methods, cell filtering and automated annotation tools.

This pipeline is written in nextflow and based on the LUCA pipeline:

Salcher, S., Sturm, G., Horvath, L., Untergasser, G., Kuempers, C., Fotakis, G., ... & Trajanoski, Z. (2022). High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer. Cancer Cell. doi:10.1016/j.ccell.2022.10.008

Overview

Created using Tennessine

Documentation

The scRAFIKI pipeline comes with documentation about preprocessing, usage and downstream analysis. It is available here.

Contact

If you encounter any problems with the pipeline or have a feature request, please use the issue tracker.