https://github.com/marrlab/car_t_targetidentification
Computational identification of targets for CAR-T cell therapy in AML
https://github.com/marrlab/car_t_targetidentification
Last synced: over 1 year ago
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Computational identification of targets for CAR-T cell therapy in AML
- Host: GitHub
- URL: https://github.com/marrlab/car_t_targetidentification
- Owner: marrlab
- License: mit
- Created: 2022-12-25T19:47:20.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2022-12-25T20:40:49.000Z (over 3 years ago)
- Last Synced: 2025-03-29T12:17:03.247Z (over 1 year ago)
- Language: Jupyter Notebook
- Size: 44.5 MB
- Stars: 16
- Watchers: 4
- Forks: 3
- Open Issues: 2
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Computational identification of targets for CAR-T cell therapy in AML
This repository contains all jupyter notebooks to reproduce the results of the single-cell data analysis from:
A. Gottschlich, M. Thomas, R. Grünmeier et al., "Single-cell transcriptomic atlas-guided development of chimeric antigen-receptor (CAR) T cells for the treatment of acute myeloid leukemia", Nature Biotechnology (2023).
The notebooks contain code for the following analyses:
- Preprocessing and Analysis of AML datasets including query to reference mapping
- Preprocessing and harmonization of single cell data across multiple organs using public datasets
- Combining public databases to infer genes coding for surface- and druggable proteins as well as analysis of bulk sequencing data
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.