scimmunity is a python tool for analyzing single-cell RNAseq data specifically for immune and cancer cells. It includes preprocessing, dimension reduction, clustering, annotation, visualization, differential expression testing, TCR analysis, and additional integration with existing single cell packages.
https://drive.google.com/drive/u/0/folders/1xiL3dBATmDDPIiG2WN-4VZixuxT4eTUH
To install the scimmunity, clone the repository and pip install in development mode.
git clone https://github.com/vdjonsson/scimmunity.git
cd scimmunity
pip install --user -e .
Prepare a samplesheet csv file with the following columns for each sample:
- sample_name:
- gex: path to cellranger count (gene) alignment
- vdj (optional): path to cellranger vdj alignment
Additional metadata columns (treatment, patient id, etc.) can be added to annotate each sample.