Multi-Omic Single-Cell Dissection of Leukemic T-Cell Lymphoma Following CAR T-Cell Therapy

This repository contains code used to produce the results in: Till Braun, Michael Rade and Maximilian Merz et al., Multi-Omic Single-Cell Dissection of Leukemic T-Cell Lymphoma Following CAR T-Cell Therapy

Contents:
- Instructions for using the singularity image and R packages can be found here: https://github.com/fraunhofer-izi/Braun_et_al_2024/tree/main/singularity
- "seurat_harmony.Rds" and "seurat_harmony_t.Rds": These Seurat objects were used to produce Figure 2 in this publication. "seurat_tcell_obj.Rds" is  a subset of "seurat_harmony.Rds" and contains only T-cells. In addition, the metadata was extended by the output of TCR-Seq (using the R package scRepertoire). The following script uses the objects: https://github.com/fraunhofer-izi/Braun_et_al_2024/blob/main/publication/figure_scripts/main/fig_02.R