Computational assessment of on-target, off-tumor toxicities of targets for CAR-T cell therapy in HL

This repository contains all jupyter notebooks to reproduce the results of the single cell cross-organ CAR T target expression analysis from:

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The notebooks contain code for the following analyses:

• Preprocessing and Harmonization of multiple public single cell RNA datasets
• Plotting expression patterns of targets for CAR-T cell therapy in HL

Note that the analysis was done in python 3 using scanpy v.1.4.6 to 1.9.1 and anndata v.0.7.1 to 0.8.0 unless otherwise stated. Some functions may have changed when using other package versions. Additionally, numpy (v. 1.18.2+), pandas (v. 1.3.5+) and scipy (v. 1.4.1+) are required. Numeric results can vary depending on package versions and e.g. minor results. All scRNA-seq figures were plotted using matplotlib and seaborn.

If the materials in this repository are of use to you, please consider citing the above publication.