SIMBA 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
Created using Tennessine
The SIMBA pipeline comes with documentation about preprocessing, usage and downstream analysis. It is available here.
If you encounter any problems with the pipeline or have a feature request, please use the issue tracker.