Notebooks used to produce results for the publication "Tumor Microenvironment Reprogramming Induced by T Cell Engager Treatment" related to the in vivo CEA-TCB MC38-huCEA data.

• Standard workflow (adapted from besca 2.4, based on scanpy)
• Cell annotation workflow (adapted from besca 2.4, based on scanpy, including exploratory analyses related to signature and marker gene expression)
• Differential expression notebook using (based on decoupler)

The underlying raw fastq, cellranger processed count matrix and processed and annotated .h5ad can be retrieved from ArrayExpress, accession nr.